rs2523870

Positions:

• chr6-31046339-C-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 0.65 in 152,028 control chromosomes in the GnomAD database, including 32,393 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 0.65 (32393 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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: 0.650 AC: 98780 AN: 151908 Hom.: 32358 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.650 AC: 98862 AN: 152028 Hom.: 32393 Cov.: 32 AF XY: 0.647 AC XY: 48081 AN XY: 74304

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.688

Alfa AF: 0.638 Hom.: 20631

Bravo AF: 0.652

Asia WGS AF: 0.639 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523870; hg19: chr6-31014116;