rs2524079

Variant names:

• chr6-31274397-G-A
• rs2524079

Your query was ambiguous. Multiple possible variants found:

• chr6-31274397-G-A
• chr6-31274397-G-C

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 0.442 in 149,986 control chromosomes in the GnomAD database, including 15,074 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 0.44 (15074 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.442 AC: 66276 AN: 149870 Hom.: 15067 Cov.: 25

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.442 AC: 66320 AN: 149986 Hom.: 15074 Cov.: 25 AF XY: 0.441 AC XY: 32265 AN XY: 73088

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.480

Alfa AF: 0.123 Hom.: 134

Bravo AF: 0.443

Asia WGS AF: 0.431 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524079; hg19: chr6-31242174;