rs10518032

Variant names:

• chr4-169026883-A-G
• rs10518032

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 0.917 in 152,142 control chromosomes in the GnomAD database, including 64,078 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 0.92 (64078 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.917 AC: 139415 AN: 152024 Hom.: 64030 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.917 AC: 139519 AN: 152142 Hom.: 64078 Cov.: 31 AF XY: 0.919 AC XY: 68362 AN XY: 74370

African (AFR) AF: 0.872 AC: 36163 AN: 41492

American (AMR) AF: 0.918 AC: 14043 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3244 AN: 3472

East Asian (EAS) AF: 0.984 AC: 5090 AN: 5174

South Asian (SAS) AF: 0.930 AC: 4471 AN: 4808

European-Finnish (FIN) AF: 0.972 AC: 10301 AN: 10596

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63065 AN: 67988

Other (OTH) AF: 0.934 AC: 1972 AN: 2112

Alfa AF: 0.921 Hom.: 11239

Bravo AF: 0.913

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.32
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10518032; hg19: chr4-169948034;