rs17157992

chr7-83720391-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 0.15 in 151,962 control chromosomes in the GnomAD database, including 4,815 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 0.15 (4815 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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: 0.150 AC: 22729 AN: 151844 Hom.: 4794 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0266

Gnomad FIN AF: 0.00595

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0234

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.150 AC: 22793 AN: 151962 Hom.: 4815 Cov.: 31 AF XY: 0.144 AC XY: 10698 AN XY: 74288

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.0769

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0264

Gnomad4 FIN AF: 0.00595

Gnomad4 NFE AF: 0.0234

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0576 Hom.: 718

Bravo AF: 0.170

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.037
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17157992; hg19: chr7-83349707;