rs3906713

Variant names:

• chr7-12180563-A-T
• rs3906713

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 0.124 in 152,150 control chromosomes in the GnomAD database, including 1,459 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 0.12 (1459 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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: 0.124 AC: 18794 AN: 152032 Hom.: 1454 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.0341

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0973

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.124 AC: 18821 AN: 152150 Hom.: 1459 Cov.: 32 AF XY: 0.120 AC XY: 8939 AN XY: 74408

African (AFR) AF: 0.222 AC: 9200 AN: 41506

American (AMR) AF: 0.0825 AC: 1260 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3470

East Asian (EAS) AF: 0.0164 AC: 85 AN: 5178

South Asian (SAS) AF: 0.0350 AC: 169 AN: 4830

European-Finnish (FIN) AF: 0.0663 AC: 703 AN: 10610

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0973 AC: 6611 AN: 67972

Other (OTH) AF: 0.118 AC: 249 AN: 2110

Alfa AF: 0.112 Hom.: 144

Bravo AF: 0.130

Asia WGS AF: 0.0410 AC: 143 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.22
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs3906713; hg19: chr7-12220189;