rs7125479

Variant names:

• chr11-108614675-A-C
• rs7125479

Your query was ambiguous. Multiple possible variants found:

• chr11-108614675-A-C
• chr11-108614675-A-G
• chr11-108614675-A-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 0.552 in 151,914 control chromosomes in the GnomAD database, including 23,310 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 0.55 (23310 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83728 AN: 151796 Hom.: 23288 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.552 AC: 83801 AN: 151914 Hom.: 23310 Cov.: 31 AF XY: 0.552 AC XY: 40962 AN XY: 74244

African (AFR) AF: 0.591 AC: 24471 AN: 41428

American (AMR) AF: 0.558 AC: 8520 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3468

East Asian (EAS) AF: 0.720 AC: 3720 AN: 5168

South Asian (SAS) AF: 0.588 AC: 2833 AN: 4814

European-Finnish (FIN) AF: 0.460 AC: 4851 AN: 10542

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35624 AN: 67932

Other (OTH) AF: 0.573 AC: 1205 AN: 2104

Alfa AF: 0.529 Hom.: 15147

Bravo AF: 0.559

Asia WGS AF: 0.654 AC: 2273 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	0.22
DANN	Benign	0.58
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7125479; hg19: chr11-108485402;