rs971517

Variant names:

• chr5-112686558-C-G
• rs971517

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 0.553 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.568

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs971517; hg19: chr5-112022255;