rs2517510

chr6-31062345-T-G

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 0.45 in 151,948 control chromosomes in the GnomAD database, including 15,705 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 0.45 (15705 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

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 (SAS) allele frequency at 95% confidence interval = 0.573 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: 0.450 AC: 68336 AN: 151830 Hom.: 15689 Cov.: 31

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.450 AC: 68384 AN: 151948 Hom.: 15705 Cov.: 31 AF XY: 0.453 AC XY: 33654 AN XY: 74264

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.506

Alfa AF: 0.419 Hom.: 7898

Bravo AF: 0.453

Asia WGS AF: 0.522 AC: 1818 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	0.77
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517510; hg19: chr6-31030122;