chr5-103578045-G-A

Variant names:

• chr5-103578045-G-A
• rs371315

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 0.371 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.512 AC: 21219 AN: 41410

American (AMR) AF: 0.299 AC: 4569 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3470

East Asian (EAS) AF: 0.762 AC: 3946 AN: 5178

South Asian (SAS) AF: 0.482 AC: 2320 AN: 4818

European-Finnish (FIN) AF: 0.207 AC: 2182 AN: 10542

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19705 AN: 67900

Other (OTH) AF: 0.376 AC: 792 AN: 2106

Alfa AF: 0.322 Hom.: 36075

Bravo AF: 0.385

Asia WGS AF: 0.607 AC: 2105 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.51
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs371315; hg19: chr5-102913746;