rs2376685

Variant names:

• chr5-118675359-C-T
• rs2376685

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 0.319 in 151,918 control chromosomes in the GnomAD database, including 9,381 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 0.32 (9381 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 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: 0.319 AC: 48431 AN: 151800 Hom.: 9352 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.319 AC: 48517 AN: 151918 Hom.: 9381 Cov.: 33 AF XY: 0.319 AC XY: 23646 AN XY: 74230

African (AFR) AF: 0.528 AC: 21851 AN: 41416

American (AMR) AF: 0.287 AC: 4377 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 543 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2850 AN: 5160

South Asian (SAS) AF: 0.225 AC: 1086 AN: 4826

European-Finnish (FIN) AF: 0.246 AC: 2592 AN: 10544

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14299 AN: 67964

Other (OTH) AF: 0.273 AC: 577 AN: 2114

Alfa AF: 0.291 Hom.: 1168

Bravo AF: 0.338

Asia WGS AF: 0.355 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.75
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2376685; hg19: chr5-118011054;