rs2531860

Positions:

• chr17-27807643-A-G
• chr17-27807643-A-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 0.77 in 152,194 control chromosomes in the GnomAD database, including 46,451 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 0.77 (46451 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117147 AN: 152076 Hom.: 46421 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.770 AC: 117227 AN: 152194 Hom.: 46451 Cov.: 32 AF XY: 0.775 AC XY: 57682 AN XY: 74396

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.778

Alfa AF: 0.819 Hom.: 67491

Bravo AF: 0.754

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.34
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2531860; hg19: chr17-26134669;