rs860465

Positions:

• chr5-143254411-A-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 0.143 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;