rs6813479

Variant names:

• chr4-136739228-T-A
• rs6813479

Your query was ambiguous. Multiple possible variants found:

• chr4-136739228-T-A
• chr4-136739228-T-C
• chr4-136739228-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.526 in 151,916 control chromosomes in the GnomAD database, including 22,011 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 0.53 (22011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.677
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79939 AN: 151798 Hom.: 21996 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.526 AC: 79982 AN: 151916 Hom.: 22011 Cov.: 32 AF XY: 0.534 AC XY: 39678 AN XY: 74252

African (AFR) AF: 0.360 AC: 14929 AN: 41430

American (AMR) AF: 0.646 AC: 9850 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1642 AN: 3466

East Asian (EAS) AF: 0.661 AC: 3412 AN: 5160

South Asian (SAS) AF: 0.672 AC: 3240 AN: 4822

European-Finnish (FIN) AF: 0.621 AC: 6547 AN: 10544

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38683 AN: 67926

Other (OTH) AF: 0.528 AC: 1115 AN: 2110

Alfa AF: 0.549 Hom.: 11914

Bravo AF: 0.519

Asia WGS AF: 0.682 AC: 2366 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.30
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs6813479; hg19: chr4-137660383;