rs860465

Variant names:

• chr5-143254411-A-G
• rs860465

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.152 AC: 6241 AN: 41024

American (AMR) AF: 0.0799 AC: 1213 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.0621 AC: 215 AN: 3460

East Asian (EAS) AF: 0.0934 AC: 476 AN: 5098

South Asian (SAS) AF: 0.0367 AC: 173 AN: 4714

European-Finnish (FIN) AF: 0.209 AC: 2100 AN: 10062

Middle Eastern (MID) AF: 0.0172 AC: 5 AN: 290

European-Non Finnish (NFE) AF: 0.157 AC: 10611 AN: 67558

Other (OTH) AF: 0.120 AC: 251 AN: 2094

Alfa AF: 0.142 Hom.: 2089

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

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