rs2376840

Positions:

• chr5-118723675-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.00972

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.0500

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.0181

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0133

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2376840; hg19: chr5-118059370;