chr6-31268398-C-T

Variant names:

• chr6-31268398-C-T
• rs2853950

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;