rs2853950

Positions:

• chr6-31268398-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 0.458 in 152,002 control chromosomes in the GnomAD database, including 16,084 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 0.46 (16084 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84

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 (AFR) allele frequency at 95% confidence interval = 0.509 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: 0.458 AC: 69583 AN: 151882 Hom.: 16077 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.458 AC: 69619 AN: 152002 Hom.: 16084 Cov.: 33 AF XY: 0.455 AC XY: 33819 AN XY: 74304

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.461

Alfa AF: 0.465 Hom.: 1604

Bravo AF: 0.471

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853950; hg19: chr6-31236175;