Genetic Variant ENST00000840728.1:n.234C>T (chr1-160647267-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000840728.1(ENSG00000228863):n.234C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0961 in 250,658 control chromosomes in the GnomAD database, including 1,743 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.094 ( 931 hom., cov: 31)

Exomes 𝑓: 0.10 ( 812 hom. )

Consequence

ENSG00000228863
ENST00000840728.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.267

Publications

13 publications found

Variant links:

Genes affected

ENSG00000228863 (HGNC:):

ENSG00000228863 links:

SLAMF1 (HGNC:10903): (signaling lymphocytic activation molecule family member 1) Enables SH2 domain binding activity and identical protein binding activity. Involved in several processes, including negative regulation of CD40 signaling pathway; negative regulation of cytokine production; and positive regulation of MAPK cascade. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

SLAMF1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLAMF1	NM_003037.5 link	c.-322G>A		upstream_gene_variant		ENST00000302035.11	NP_003028.1	Q13291-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000228863	ENST00000840728.1 link	n.234C>T	non_coding_transcript_exon_variant	Exon 1 of 2
SLAMF1	ENST00000302035.11 link	c.-322G>A	upstream_gene_variant		1	NM_003037.5	ENSP00000306190.6	Q13291-1
SLAMF1	ENST00000494463.1 link	n.-246G>A	upstream_gene_variant		1
ENSG00000228863	ENST00000840727.1 link	n.-19C>T	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0939

AC:

14270

AN:

152012

Hom.:

929

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0912

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.0965

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0706

Gnomad OTH

AF:

0.0920

GnomAD4 exome

AF:

0.0995

AC:

9805

AN:

98528

Hom.:

812

Cov.:

AF XY:

0.0979

AC XY:

5156

AN XY:

52656

show subpopulations

African (AFR)

AF:

0.0775

AC:

317

AN:

4090

American (AMR)

AF:

0.107

AC:

717

AN:

6672

Ashkenazi Jewish (ASJ)

AF:

0.0358

AC:

AN:

2456

East Asian (EAS)

AF:

0.362

AC:

2408

AN:

6654

South Asian (SAS)

AF:

0.0861

AC:

1373

AN:

15952

European-Finnish (FIN)

AF:

0.128

AC:

457

AN:

3576

Middle Eastern (MID)

AF:

0.0437

AC:

AN:

320

European-Non Finnish (NFE)

AF:

0.0744

AC:

4006

AN:

53860

Other (OTH)

AF:

0.0859

AC:

425

AN:

4948

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

380

760

1140

1520

1900

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

184

276

368

460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0939

AC:

14291

AN:

152130

Hom.:

931

Cov.:

AF XY:

0.0977

AC XY:

7263

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.0914

AC:

3794

AN:

41502

American (AMR)

AF:

0.105

AC:

1610

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0297

AC:

103

AN:

3470

East Asian (EAS)

AF:

0.366

AC:

1890

AN:

5158

South Asian (SAS)

AF:

0.0966

AC:

466

AN:

4824

European-Finnish (FIN)

AF:

0.134

AC:

1412

AN:

10570

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0706

AC:

4802

AN:

68000

Other (OTH)

AF:

0.0944

AC:

199

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

637

1274

1911

2548

3185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0667

Hom.:

499

Bravo

AF:

0.0917

Asia WGS

AF:

0.192

AC:

667

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.4

(source)

DANN

Benign

0.62

PhyloP100

-0.27

PromoterAI

-0.13

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over