rs972317

Variant names:

• chr17-36044622-T-G
• rs972317

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 0.13 in 152,234 control chromosomes in the GnomAD database, including 1,422 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 0.13 (1422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 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: 0.129 AC: 19684 AN: 152116 Hom.: 1417 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.130 AC: 19717 AN: 152234 Hom.: 1422 Cov.: 32 AF XY: 0.134 AC XY: 10003 AN XY: 74438

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0682

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.141

Alfa AF: 0.120 Hom.: 1565

Bravo AF: 0.133

Asia WGS AF: 0.144 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.90
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs972317; hg19: chr17-34371659;