rs1931475

Variant names:

• chr13-71375401-C-T
• rs1931475

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 0.017 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 49 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: 0.0170 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

African (AFR) AF: 0.0403 AC: 1672 AN: 41528

American (AMR) AF: 0.0245 AC: 375 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3470

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5180

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4818

European-Finnish (FIN) AF: 0.000568 AC: 6 AN: 10572

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00448 AC: 305 AN: 68022

Other (OTH) AF: 0.0152 AC: 32 AN: 2112

Alfa AF: 0.00888 Hom.: 9

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
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs1931475; hg19: chr13-71949533;