rs10518292

Variant names:

• chr4-118364120-G-A
• rs10518292

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0106

Gnomad4 AMR AF: 0.0551

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.0668

Gnomad4 NFE AF: 0.0550

Gnomad4 OTH AF: 0.0441

Alfa AF: 0.0432 Hom.: 27

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518292; hg19: chr4-119285275;