rs2524276

chr6-31440488-C-A

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 0.0673 in 151,824 control chromosomes in the GnomAD database, including 552 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 0.067 (552 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0885 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: 0.0673 AC: 10207 AN: 151706 Hom.: 551 Cov.: 31

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.00965

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.00727

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.0673 AC: 10218 AN: 151824 Hom.: 552 Cov.: 31 AF XY: 0.0646 AC XY: 4791 AN XY: 74212

Gnomad4 AFR AF: 0.0855

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.00986

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.00727

Gnomad4 NFE AF: 0.0644

Gnomad4 OTH AF: 0.0893

Alfa AF: 0.0609 Hom.: 420

Bravo AF: 0.0763

Asia WGS AF: 0.0470 AC: 161 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.8
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524276; hg19: chr6-31408265;