6-31580015-C-T

Variant names:

• chr6-31580015-C-T
• rs3093559

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0248 in 152,296 control chromosomes in the GnomAD database, including 56 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 0.025 (56 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0248 (3779/152296) while in subpopulation AFR AF = 0.037 (1538/41552). AF 95% confidence interval is 0.0355. There are 56 homozygotes in GnomAd4. There are 1749 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 56 gene

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: 0.0248 AC: 3772 AN: 152178 Hom.: 56 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0248 AC: 3779 AN: 152296 Hom.: 56 Cov.: 32 AF XY: 0.0235 AC XY: 1749 AN XY: 74470

African (AFR) AF: 0.0370 AC: 1538 AN: 41552

American (AMR) AF: 0.0235 AC: 360 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0689 AC: 239 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0120 AC: 58 AN: 4824

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10620

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0212 AC: 1443 AN: 68030

Other (OTH) AF: 0.0289 AC: 61 AN: 2108

Alfa AF: 0.0236 Hom.: 149

Bravo AF: 0.0278

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.73
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs3093559; hg19: chr6-31547792;