rs625487

Positions:

• chr5-41561271-C-A
• chr5-41561271-C-G

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 0.534 in 151,816 control chromosomes in the GnomAD database, including 23,956 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 0.53 (23956 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41561271C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80959 AN: 151698 Hom.: 23930 Cov.: 30

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.534 AC: 81023 AN: 151816 Hom.: 23956 Cov.: 30 AF XY: 0.536 AC XY: 39740 AN XY: 74206

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.534

Alfa AF: 0.624 Hom.: 28676

Bravo AF: 0.519

Asia WGS AF: 0.470 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs625487; hg19: chr5-41561373;