rs2381958

Variant names:

• chr5-175082883-G-A
• rs2381958

Your query was ambiguous. Multiple possible variants found:

• chr5-175082883-G-A
• chr5-175082883-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.228 in 152,050 control chromosomes in the GnomAD database, including 4,528 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 0.23 (4528 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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: 0.228 AC: 34646 AN: 151932 Hom.: 4522 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.228 AC: 34682 AN: 152050 Hom.: 4528 Cov.: 33 AF XY: 0.231 AC XY: 17141 AN XY: 74304

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.225

Alfa AF: 0.185 Hom.: 1326

Bravo AF: 0.242

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2381958; hg19: chr5-174509886;