rs2523685

chr6-31458479-G-Cchr6-31458479-G-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 0.322 in 151,502 control chromosomes in the GnomAD database, including 9,257 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 0.32 (9257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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: 0.322 AC: 48741 AN: 151386 Hom.: 9220 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.322 AC: 48825 AN: 151502 Hom.: 9257 Cov.: 32 AF XY: 0.325 AC XY: 24048 AN XY: 74048

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.361

Alfa AF: 0.142 Hom.: 272

Bravo AF: 0.341

Asia WGS AF: 0.303 AC: 1046 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.17
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523685; hg19: chr6-31426256;