rs10518292

chr4-118364120-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;