rs7662116

chr4-153096812-C-A

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 0.616 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.606

Alfa AF: 0.689 Hom.: 49533

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7662116; hg19: chr4-154017964;