18-8966146-G-T

Variant names:

• chr18-8966146-G-T
• rs10502386

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 0.387 in 152,004 control chromosomes in the GnomAD database, including 12,037 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 0.39 (12037 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 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: 0.387 AC: 58753 AN: 151886 Hom.: 12027 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.387 AC: 58800 AN: 152004 Hom.: 12037 Cov.: 32 AF XY: 0.383 AC XY: 28437 AN XY: 74310

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.404

Alfa AF: 0.457 Hom.: 32761

Bravo AF: 0.377

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
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: rs10502386; hg19: chr18-8966144;