rs10464063

Variant names:

• chr5-180652970-C-T
• rs10464063

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 0.442 in 152,070 control chromosomes in the GnomAD database, including 14,976 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 0.44 (14976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67067 AN: 151952 Hom.: 14951 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.442 AC: 67140 AN: 152070 Hom.: 14976 Cov.: 32 AF XY: 0.443 AC XY: 32917 AN XY: 74326

African (AFR) AF: 0.359 AC: 14898 AN: 41468

American (AMR) AF: 0.462 AC: 7056 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1675 AN: 3472

East Asian (EAS) AF: 0.560 AC: 2890 AN: 5162

South Asian (SAS) AF: 0.513 AC: 2476 AN: 4828

European-Finnish (FIN) AF: 0.443 AC: 4674 AN: 10556

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32066 AN: 67976

Other (OTH) AF: 0.440 AC: 930 AN: 2114

Alfa AF: 0.465 Hom.: 2750

Bravo AF: 0.444

Asia WGS AF: 0.505 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.81
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10464063; hg19: chr5-180079970;