chr5-31375946-C-T

Variant names:

• chr5-31375946-C-T
• rs13186629

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.294 in 152,110 control chromosomes in the GnomAD database, including 7,554 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 0.29 (7554 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

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: 0.294 AC: 44760 AN: 151992 Hom.: 7549 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.294 AC: 44764 AN: 152110 Hom.: 7554 Cov.: 32 AF XY: 0.292 AC XY: 21702 AN XY: 74370

African (AFR) AF: 0.129 AC: 5376 AN: 41528

American (AMR) AF: 0.327 AC: 4996 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1253 AN: 5182

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4814

European-Finnish (FIN) AF: 0.307 AC: 3239 AN: 10558

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25982 AN: 67956

Other (OTH) AF: 0.322 AC: 680 AN: 2110

Alfa AF: 0.358 Hom.: 40165

Bravo AF: 0.292

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.5
DANN	Benign	0.59
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs13186629; hg19: chr5-31376053;