3-11915124-A-G

Variant names:

• chr3-11915124-A-G
• rs6777876

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 0.0988 in 152,118 control chromosomes in the GnomAD database, including 765 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 0.099 (765 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 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: 0.0988 AC: 15023 AN: 152002 Hom.: 765 Cov.: 32

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0988 AC: 15031 AN: 152118 Hom.: 765 Cov.: 32 AF XY: 0.0988 AC XY: 7346 AN XY: 74364

African (AFR) AF: 0.0838 AC: 3478 AN: 41502

American (AMR) AF: 0.0727 AC: 1112 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0874 AC: 303 AN: 3466

East Asian (EAS) AF: 0.0568 AC: 293 AN: 5160

South Asian (SAS) AF: 0.149 AC: 719 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10604

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7679 AN: 67958

Other (OTH) AF: 0.0848 AC: 179 AN: 2112

Alfa AF: 0.105 Hom.: 2557

Bravo AF: 0.0933

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.087
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs6777876; hg19: chr3-11956598;