rs10518292

Variant names:

• chr4-118364120-G-A
• rs10518292

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 0.04 in 152,170 control chromosomes in the GnomAD database, including 172 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 0.040 (172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0536 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: 0.0401 AC: 6094 AN: 152052 Hom.: 172 Cov.: 32

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0552

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0400 AC: 6093 AN: 152170 Hom.: 172 Cov.: 32 AF XY: 0.0391 AC XY: 2908 AN XY: 74380

African (AFR) AF: 0.0106 AC: 439 AN: 41534

American (AMR) AF: 0.0551 AC: 842 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4822

European-Finnish (FIN) AF: 0.0668 AC: 706 AN: 10568

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3743 AN: 67994

Other (OTH) AF: 0.0441 AC: 93 AN: 2108

Alfa AF: 0.0323 Hom.: 32

Bravo AF: 0.0391

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.51
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10518292; hg19: chr4-119285275;