6-31083611-C-T

Variant names:

• chr6-31083611-C-T
• rs2535318

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 0.45 in 151,728 control chromosomes in the GnomAD database, including 15,666 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 0.45 (15666 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 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: 0.450 AC: 68247 AN: 151608 Hom.: 15649 Cov.: 30

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.450 AC: 68293 AN: 151728 Hom.: 15666 Cov.: 30 AF XY: 0.454 AC XY: 33626 AN XY: 74136

African (AFR) AF: 0.506 AC: 20933 AN: 41340

American (AMR) AF: 0.479 AC: 7308 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2234 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2445 AN: 5156

South Asian (SAS) AF: 0.591 AC: 2846 AN: 4814

European-Finnish (FIN) AF: 0.432 AC: 4533 AN: 10484

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.389 AC: 26403 AN: 67914

Other (OTH) AF: 0.504 AC: 1062 AN: 2108

Alfa AF: 0.416 Hom.: 13819

Bravo AF: 0.453

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.51
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs2535318; hg19: chr6-31051388;