dbSNP rs6474491: ENSG00000253356:n.100-6980T>C (chr8-38156330-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000520598.1(ENSG00000253356):n.100-6980T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,010 control chromosomes in the GnomAD database, including 4,759 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 0.25 ( 4759 hom., cov: 31)

Consequence

ENSG00000253356
ENST00000520598.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.164

Publications

11 publications found

Variant links:

Genes affected

ENSG00000253356 (HGNC:):

ENSG00000253356 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379382	XR_949687.2 link	n.-9T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253356	ENST00000520598.1 link	n.100-6980T>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37395

AN:

151890

Hom.:

4761

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.324

Gnomad AMR

AF:

0.218

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.208

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.253

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.246

AC:

37419

AN:

152010

Hom.:

4759

Cov.:

AF XY:

0.247

AC XY:

18362

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.233

AC:

9648

AN:

41430

American (AMR)

AF:

0.218

AC:

3328

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.270

AC:

937

AN:

3470

East Asian (EAS)

AF:

0.332

AC:

1716

AN:

5170

South Asian (SAS)

AF:

0.382

AC:

1841

AN:

4818

European-Finnish (FIN)

AF:

0.208

AC:

2200

AN:

10574

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.247

AC:

16818

AN:

67980

Other (OTH)

AF:

0.256

AC:

539

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1448

2896

4345

5793

7241

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<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:

0.252

Hom.:

10550

Bravo

AF:

0.243

Asia WGS

AF:

0.344

AC:

1197

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.6

(source)

DANN

Benign

0.67

PhyloP100

0.16

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