chr5-31391299-T-C

Variant names:

• chr5-31391299-T-C
• rs669702

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 0.86 in 151,770 control chromosomes in the GnomAD database, including 56,713 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 0.86 (56713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 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: 0.860 AC: 130431 AN: 151652 Hom.: 56672 Cov.: 32

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.860 AC: 130521 AN: 151770 Hom.: 56713 Cov.: 32 AF XY: 0.854 AC XY: 63351 AN XY: 74206

African (AFR) AF: 0.873 AC: 35921 AN: 41124

American (AMR) AF: 0.777 AC: 11876 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2695 AN: 3472

East Asian (EAS) AF: 0.571 AC: 2952 AN: 5168

South Asian (SAS) AF: 0.720 AC: 3463 AN: 4810

European-Finnish (FIN) AF: 0.885 AC: 9366 AN: 10586

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61442 AN: 68024

Other (OTH) AF: 0.846 AC: 1786 AN: 2110

Alfa AF: 0.881 Hom.: 30078

Bravo AF: 0.853

Asia WGS AF: 0.630 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.75
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs669702; hg19: chr5-31391406;