rs1931475

Positions:

• chr13-71375401-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 0.017 in 152,188 control chromosomes in the GnomAD database, including 49 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 0.017 (49 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.017 (2593/152188) while in subpopulation AFR AF= 0.0403 (1672/41528). AF 95% confidence interval is 0.0387. There are 49 homozygotes in gnomad4. There are 1260 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 49 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0170 AC: 2586 AN: 152070 Hom.: 49 Cov.: 33

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.000568

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00447

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0170 AC: 2593 AN: 152188 Hom.: 49 Cov.: 33 AF XY: 0.0169 AC XY: 1260 AN XY: 74398

Gnomad4 AFR AF: 0.0403

Gnomad4 AMR AF: 0.0245

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.000568

Gnomad4 NFE AF: 0.00448

Gnomad4 OTH AF: 0.0152

Alfa AF: 0.00823 Hom.: 4

Bravo AF: 0.0206

Asia WGS AF: 0.0150 AC: 53 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1931475; hg19: chr13-71949533;