rs2508011

Positions:

• chr6-31103281-A-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 0.369 in 151,904 control chromosomes in the GnomAD database, including 10,752 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 0.37 (10752 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55973 AN: 151786 Hom.: 10740 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.369 AC: 56016 AN: 151904 Hom.: 10752 Cov.: 31 AF XY: 0.365 AC XY: 27141 AN XY: 74280

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.403

Alfa AF: 0.357 Hom.: 4122

Bravo AF: 0.373

Asia WGS AF: 0.248 AC: 864 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	2.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2508011; hg19: chr6-31071058;