rs3093559

Positions:

• chr6-31580015-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 0.0248 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 56 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31580015C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.0235

Gnomad4 ASJ AF: 0.0689

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.0212

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0275 Hom.: 67

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093559; hg19: chr6-31547792;