18-10626554-G-T

Position:

• chr18-10626554-G-T

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 0.41 in 152,094 control chromosomes in the GnomAD database, including 13,073 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 0.41 (13073 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62331 AN: 151976 Hom.: 13063 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.410 AC: 62373 AN: 152094 Hom.: 13073 Cov.: 32 AF XY: 0.411 AC XY: 30555 AN XY: 74352

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.452

Alfa AF: 0.412 Hom.: 5914

Bravo AF: 0.412

Asia WGS AF: 0.544 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2276371; hg19: chr18-10626551; COSMIC: COSV73839434;