rs2156875

Positions:

• chr6-31349570-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 0.5 in 151,972 control chromosomes in the GnomAD database, including 19,063 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 0.50 (19063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

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 (NFE) allele frequency at 95% confidence interval = 0.508 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: 0.500 AC: 75883 AN: 151854 Hom.: 19055 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.500 AC: 75934 AN: 151972 Hom.: 19063 Cov.: 32 AF XY: 0.495 AC XY: 36784 AN XY: 74274

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.464

Alfa AF: 0.505 Hom.: 30578

Bravo AF: 0.491

Asia WGS AF: 0.517 AC: 1798 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	8.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2156875; hg19: chr6-31317347;