rs371315

Positions:

• chr5-103578045-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;