rs2376840

Variant names:

• chr5-118723675-T-G
• rs2376840

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 0.0146 in 152,304 control chromosomes in the GnomAD database, including 26 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 0.015 (26 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0146 (2217/152304) while in subpopulation EAS AF = 0.05 (259/5180). AF 95% confidence interval is 0.045. There are 26 homozygotes in GnomAd4. There are 1117 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 26 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: 0.0145 AC: 2207 AN: 152186 Hom.: 23 Cov.: 33

Gnomad AFR AF: 0.00974

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.0161

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0129

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

GnomAD4 genome AF: 0.0146 AC: 2217 AN: 152304 Hom.: 26 Cov.: 33 AF XY: 0.0150 AC XY: 1117 AN XY: 74470

African (AFR) AF: 0.00972 AC: 404 AN: 41580

American (AMR) AF: 0.0271 AC: 415 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.0500 AC: 259 AN: 5180

South Asian (SAS) AF: 0.0164 AC: 79 AN: 4830

European-Finnish (FIN) AF: 0.0181 AC: 192 AN: 10624

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0112 AC: 764 AN: 68018

Other (OTH) AF: 0.0133 AC: 28 AN: 2112

Alfa AF: 0.0140 Hom.: 2

Bravo AF: 0.0178

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.53
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs2376840; hg19: chr5-118059370;