rs860465

Variant names:

• chr5-143254411-A-G
• rs860465

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 0.143 in 150,380 control chromosomes in the GnomAD database, including 1,674 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 0.14 (1674 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 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: 0.143 AC: 21461 AN: 150270 Hom.: 1668 Cov.: 28

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.0800

Gnomad ASJ AF: 0.0621

Gnomad EAS AF: 0.0933

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.0192

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.143 AC: 21506 AN: 150380 Hom.: 1674 Cov.: 28 AF XY: 0.142 AC XY: 10401 AN XY: 73438

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0799

Gnomad4 ASJ AF: 0.0621

Gnomad4 EAS AF: 0.0934

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.120

Alfa AF: 0.141 Hom.: 1611

Bravo AF: 0.136

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs860465; hg19: chr5-142633976; COSMIC: COSV67249512;