6-31286101-C-T

Variant names:

• chr6-31286101-C-T
• rs2853935

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 0.658 in 152,078 control chromosomes in the GnomAD database, including 33,208 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 0.66 (33208 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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: 0.657 AC: 99907 AN: 151960 Hom.: 33167 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.658 AC: 100001 AN: 152078 Hom.: 33208 Cov.: 32 AF XY: 0.662 AC XY: 49239 AN XY: 74350

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.681

Alfa AF: 0.619 Hom.: 9469

Bravo AF: 0.666

Asia WGS AF: 0.714 AC: 2482 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	3.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853935; hg19: chr6-31253878;