rs916864

chr7-95357648-C-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 0.184 in 152,212 control chromosomes in the GnomAD database, including 3,572 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 0.18 (3572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.894

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 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: 0.184 AC: 28035 AN: 152094 Hom.: 3570 Cov.: 32

Gnomad AFR AF: 0.0654

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.184 AC: 28041 AN: 152212 Hom.: 3572 Cov.: 32 AF XY: 0.190 AC XY: 14170 AN XY: 74430

Gnomad4 AFR AF: 0.0652

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.204

Alfa AF: 0.206 Hom.: 3349

Bravo AF: 0.197

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.5
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916864; hg19: chr7-94986960;