rs2396676

Variant names:

• chr7-113687111-G-A
• rs2396676

Your query was ambiguous. Multiple possible variants found:

• chr7-113687111-G-A
• chr7-113687111-G-C
• chr7-113687111-G-T

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 0.399 in 152,004 control chromosomes in the GnomAD database, including 16,809 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 0.40 (16809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 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: 0.398 AC: 60476 AN: 151886 Hom.: 16755 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.399 AC: 60605 AN: 152004 Hom.: 16809 Cov.: 32 AF XY: 0.396 AC XY: 29438 AN XY: 74308

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.376

Alfa AF: 0.245 Hom.: 10940

Bravo AF: 0.425

Asia WGS AF: 0.339 AC: 1180 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	0.034
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2396676; hg19: chr7-113327166;