rs2524079

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;