6-31084350-C-T

Variant names:

• chr6-31084350-C-T
• rs2535315

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 0.434 in 151,970 control chromosomes in the GnomAD database, including 14,546 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 0.43 (14546 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 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: 0.435 AC: 65988 AN: 151852 Hom.: 14536 Cov.: 31

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.434 AC: 66025 AN: 151970 Hom.: 14546 Cov.: 31 AF XY: 0.439 AC XY: 32577 AN XY: 74268

African (AFR) AF: 0.465 AC: 19269 AN: 41438

American (AMR) AF: 0.466 AC: 7115 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2219 AN: 3466

East Asian (EAS) AF: 0.475 AC: 2442 AN: 5146

South Asian (SAS) AF: 0.586 AC: 2816 AN: 4808

European-Finnish (FIN) AF: 0.429 AC: 4530 AN: 10568

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26106 AN: 67962

Other (OTH) AF: 0.482 AC: 1014 AN: 2104

Alfa AF: 0.415 Hom.: 15429

Bravo AF: 0.435

Asia WGS AF: 0.513 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2535315; hg19: chr6-31052127;