Genetic Variant ENSG00000261821:n.3359C>T (chr15-74369553-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 ENST00000568496.3(ENSG00000261821):n.3359C>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 0.28 in 152,162 control chromosomes in the GnomAD database, including 7,865 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 0.28 ( 7861 hom., cov: 32)

Exomes 𝑓: 0.25 ( 4 hom. )

Consequence

ENSG00000261821
ENST00000568496.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400

Publications

11 publications found

Variant links:

Genes affected

ENSG00000261821 (HGNC:):

ENSG00000261821 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903524	XR_007064709.1 link	n.3936C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000261821	ENST00000568496.3 link	n.3359C>T	non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000261821	ENST00000783990.1 link	n.478-928C>T	intron_variant	Intron 2 of 2
ENSG00000261821	ENST00000783991.1 link	n.553-928C>T	intron_variant	Intron 1 of 1
ENSG00000302041	ENST00000783573.1 link	n.*228G>A	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42516

AN:

152000

Hom.:

7831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.434

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.253

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.214

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.300

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.280

AC:

42612

AN:

152118

Hom.:

7861

Cov.:

AF XY:

0.281

AC XY:

20904

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.518

AC:

21475

AN:

41442

American (AMR)

AF:

0.219

AC:

3354

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.193

AC:

671

AN:

3468

East Asian (EAS)

AF:

0.435

AC:

2250

AN:

5178

South Asian (SAS)

AF:

0.382

AC:

1842

AN:

4822

European-Finnish (FIN)

AF:

0.171

AC:

1806

AN:

10590

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.153

AC:

10426

AN:

68018

Other (OTH)

AF:

0.258

AC:

544

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1393

2786

4179

5572

6965

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.200

Hom.:

12026

Bravo

AF:

0.293

Asia WGS

AF:

0.438

AC:

1524

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.9

(source)

DANN

Benign

0.53

PhyloP100

-0.040

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over