rs620876

Variant names:

• chr5-41581411-G-A
• rs620876

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 0.103 in 152,188 control chromosomes in the GnomAD database, including 960 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 0.10 (960 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.103 AC: 15650 AN: 152070 Hom.: 958 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.0637

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.103 AC: 15653 AN: 152188 Hom.: 960 Cov.: 32 AF XY: 0.100 AC XY: 7449 AN XY: 74422

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.0629

Gnomad4 FIN AF: 0.0469

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0991 Hom.: 143

Bravo AF: 0.110

Asia WGS AF: 0.0500 AC: 174 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs620876; hg19: chr5-41581513;