rs10464059

Variant names:

• chr5-180367208-G-A
• rs10464059

Your query was ambiguous. Multiple possible variants found:

• chr5-180367208-G-A
• chr5-180367208-G-C

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 0.207 in 152,030 control chromosomes in the GnomAD database, including 3,681 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 0.21 (3681 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 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: 0.207 AC: 31385 AN: 151912 Hom.: 3665 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.207 AC: 31443 AN: 152030 Hom.: 3681 Cov.: 32 AF XY: 0.208 AC XY: 15471 AN XY: 74304

African (AFR) AF: 0.318 AC: 13172 AN: 41442

American (AMR) AF: 0.138 AC: 2108 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5164

South Asian (SAS) AF: 0.233 AC: 1117 AN: 4804

European-Finnish (FIN) AF: 0.190 AC: 2002 AN: 10564

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10340 AN: 68006

Other (OTH) AF: 0.202 AC: 426 AN: 2112

Alfa AF: 0.173 Hom.: 10367

Bravo AF: 0.205

Asia WGS AF: 0.288 AC: 966 AN: 3358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.83
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10464059; hg19: chr5-179794208;