rs7662116

Variant names:

• chr4-153096812-C-A
• rs7662116

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 0.616 in 152,012 control chromosomes in the GnomAD database, including 30,296 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 0.62 (30296 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 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: 0.616 AC: 93561 AN: 151894 Hom.: 30292 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.616 AC: 93581 AN: 152012 Hom.: 30296 Cov.: 31 AF XY: 0.616 AC XY: 45785 AN XY: 74310

African (AFR) AF: 0.416 AC: 17233 AN: 41412

American (AMR) AF: 0.556 AC: 8490 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2645 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3371 AN: 5182

South Asian (SAS) AF: 0.704 AC: 3391 AN: 4816

European-Finnish (FIN) AF: 0.754 AC: 7968 AN: 10572

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48406 AN: 67980

Other (OTH) AF: 0.606 AC: 1280 AN: 2112

Alfa AF: 0.676 Hom.: 66490

Bravo AF: 0.591

Asia WGS AF: 0.653 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.64
DANN	Benign	0.18
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs7662116; hg19: chr4-154017964;