6-31579643-C-T

Position:

• chr6-31579643-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.00975 in 152,296 control chromosomes in the GnomAD database, including 6 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 0.0098 (6 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.784

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00975 (1485/152296) while in subpopulation SAS AF= 0.0313 (151/4826). AF 95% confidence interval is 0.0272. There are 6 homozygotes in gnomad4. There are 758 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31579643C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00974 AC: 1482 AN: 152178 Hom.: 6 Cov.: 32

Gnomad AFR AF: 0.00565

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.00752

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.00499

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.00812

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

GnomAD4 genome AF: 0.00975 AC: 1485 AN: 152296 Hom.: 6 Cov.: 32 AF XY: 0.0102 AC XY: 758 AN XY: 74464

Gnomad4 AFR AF: 0.00565

Gnomad4 AMR AF: 0.00751

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.0313

Gnomad4 FIN AF: 0.00499

Gnomad4 NFE AF: 0.0119

Gnomad4 OTH AF: 0.00803

Alfa AF: 0.0105 Hom.: 1

Bravo AF: 0.00883

Asia WGS AF: 0.0230 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093672; hg19: chr6-31547420;