rs2381958

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;