5-18518460-G-T

Variant names:

• chr5-18518460-G-T
• rs10942238

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 0.714 in 151,818 control chromosomes in the GnomAD database, including 40,017 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 0.71 (40017 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.714 AC: 108376 AN: 151700 Hom.: 39995 Cov.: 31

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.714 AC: 108440 AN: 151818 Hom.: 40017 Cov.: 31 AF XY: 0.717 AC XY: 53218 AN XY: 74192

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.736

Alfa AF: 0.768 Hom.: 26055

Bravo AF: 0.713

Asia WGS AF: 0.873 AC: 3034 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10942238; hg19: chr5-18518569;