5-6196931-T-C

Variant names:

• chr5-6196931-T-C
• rs2937785

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 0.869 in 152,132 control chromosomes in the GnomAD database, including 57,850 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 0.87 (57850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 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: 0.869 AC: 132120 AN: 152016 Hom.: 57813 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.869 AC: 132213 AN: 152132 Hom.: 57850 Cov.: 32 AF XY: 0.871 AC XY: 64773 AN XY: 74378

African (AFR) AF: 0.764 AC: 31700 AN: 41482

American (AMR) AF: 0.908 AC: 13882 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3042 AN: 3470

East Asian (EAS) AF: 0.950 AC: 4908 AN: 5168

South Asian (SAS) AF: 0.848 AC: 4078 AN: 4808

European-Finnish (FIN) AF: 0.926 AC: 9825 AN: 10610

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61772 AN: 67982

Other (OTH) AF: 0.878 AC: 1856 AN: 2114

Alfa AF: 0.895 Hom.: 236927

Bravo AF: 0.864

Asia WGS AF: 0.901 AC: 3134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.16
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs2937785; hg19: chr5-6197044;