rs371315

Variant names:

• chr5-103578045-G-A
• rs371315

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 0.371 in 151,894 control chromosomes in the GnomAD database, including 11,816 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 0.37 (11816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.371 AC: 56340 AN: 151774 Hom.: 11799 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.371 AC: 56409 AN: 151894 Hom.: 11816 Cov.: 32 AF XY: 0.371 AC XY: 27533 AN XY: 74230

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.376

Alfa AF: 0.312 Hom.: 15686

Bravo AF: 0.385

Asia WGS AF: 0.607 AC: 2105 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs371315; hg19: chr5-102913746;