rs4975616

chr5-1315545-G-Achr5-1315545-G-Cchr5-1315545-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 0.522 in 152,090 control chromosomes in the GnomAD database, including 22,663 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 0.52 (22663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79318 AN: 151972 Hom.: 22657 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.522 AC: 79355 AN: 152090 Hom.: 22663 Cov.: 32 AF XY: 0.531 AC XY: 39444 AN XY: 74328

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.561

Alfa AF: 0.582 Hom.: 60569

Bravo AF: 0.517

Asia WGS AF: 0.762 AC: 2648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4975616; hg19: chr5-1315660;