rs685478

Variant names:

• chr11-112806159-C-A
• rs685478

Your query was ambiguous. Multiple possible variants found:

• chr11-112806159-C-A
• chr11-112806159-C-G
• chr11-112806159-C-T

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 0.471 in 151,842 control chromosomes in the GnomAD database, including 17,506 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 0.47 (17506 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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: 0.470 AC: 71372 AN: 151724 Hom.: 17466 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.471 AC: 71468 AN: 151842 Hom.: 17506 Cov.: 31 AF XY: 0.478 AC XY: 35456 AN XY: 74182

African (AFR) AF: 0.576 AC: 23849 AN: 41402

American (AMR) AF: 0.486 AC: 7429 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3468

East Asian (EAS) AF: 0.688 AC: 3538 AN: 5142

South Asian (SAS) AF: 0.571 AC: 2742 AN: 4798

European-Finnish (FIN) AF: 0.446 AC: 4701 AN: 10530

Middle Eastern (MID) AF: 0.424 AC: 123 AN: 290

European-Non Finnish (NFE) AF: 0.390 AC: 26462 AN: 67908

Other (OTH) AF: 0.463 AC: 974 AN: 2102

Alfa AF: 0.412 Hom.: 4263

Bravo AF: 0.477

Asia WGS AF: 0.621 AC: 2161 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.86
DANN	Benign	0.60
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs685478; hg19: chr11-112676882;