6-31268398-C-T

Variant names:

• chr6-31268398-C-T
• rs2853950

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.514 AC: 21307 AN: 41424

American (AMR) AF: 0.451 AC: 6891 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1893 AN: 3466

East Asian (EAS) AF: 0.476 AC: 2462 AN: 5172

South Asian (SAS) AF: 0.413 AC: 1989 AN: 4820

European-Finnish (FIN) AF: 0.351 AC: 3701 AN: 10546

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29846 AN: 67984

Other (OTH) AF: 0.461 AC: 971 AN: 2108

Alfa AF: 0.453 Hom.: 14327

Bravo AF: 0.471

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.52
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2853950; hg19: chr6-31236175;