chr6-31579012-T-C

Variant names:

• chr6-31579012-T-C
• rs3093726

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 0.0283 in 152,310 control chromosomes in the GnomAD database, including 67 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 0.028 (67 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0283 (4314/152310) while in subpopulation SAS AF = 0.0524 (253/4830). AF 95% confidence interval is 0.0471. There are 67 homozygotes in GnomAd4. There are 2076 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 67 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: 0.0283 AC: 4313 AN: 152192 Hom.: 68 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0154

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.00999

Gnomad SAS AF: 0.0534

Gnomad FIN AF: 0.00979

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0283 AC: 4314 AN: 152310 Hom.: 67 Cov.: 32 AF XY: 0.0279 AC XY: 2076 AN XY: 74462

African (AFR) AF: 0.0189 AC: 785 AN: 41558

American (AMR) AF: 0.0154 AC: 235 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3470

East Asian (EAS) AF: 0.0100 AC: 52 AN: 5192

South Asian (SAS) AF: 0.0524 AC: 253 AN: 4830

European-Finnish (FIN) AF: 0.00979 AC: 104 AN: 10620

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0373 AC: 2536 AN: 68030

Other (OTH) AF: 0.0289 AC: 61 AN: 2110

Alfa AF: 0.0302 Hom.: 17

Bravo AF: 0.0280

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.57
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs3093726; hg19: chr6-31546789;