rs971517

Variant names:

• chr5-112686558-C-G
• rs971517

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 0.553 in 151,934 control chromosomes in the GnomAD database, including 23,771 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 0.55 (23771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 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: 0.553 AC: 84007 AN: 151816 Hom.: 23753 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.553 AC: 84073 AN: 151934 Hom.: 23771 Cov.: 32 AF XY: 0.555 AC XY: 41247 AN XY: 74270

African (AFR) AF: 0.542 AC: 22430 AN: 41366

American (AMR) AF: 0.628 AC: 9585 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1781 AN: 3468

East Asian (EAS) AF: 0.817 AC: 4233 AN: 5180

South Asian (SAS) AF: 0.650 AC: 3134 AN: 4822

European-Finnish (FIN) AF: 0.466 AC: 4914 AN: 10548

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36163 AN: 67974

Other (OTH) AF: 0.568 AC: 1199 AN: 2110

Alfa AF: 0.530 Hom.: 2701

Bravo AF: 0.569

Asia WGS AF: 0.723 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.53
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs971517; hg19: chr5-112022255;