3-11915124-A-G

Variant names:

• chr3-11915124-A-G
• rs6777876

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0988 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

Gnomad4 AFR AF: 0.0838

Gnomad4 AMR AF: 0.0727

Gnomad4 ASJ AF: 0.0874

Gnomad4 EAS AF: 0.0568

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0848

Alfa AF: 0.106 Hom.: 985

Bravo AF: 0.0933

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6777876; hg19: chr3-11956598;