18-38101978-A-C

Position:

• chr18-38101978-A-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.095 in 152,260 control chromosomes in the GnomAD database, including 1,839 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 0.095 (1839 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.65

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 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: 0.0947 AC: 14415 AN: 152142 Hom.: 1826 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0950 AC: 14466 AN: 152260 Hom.: 1839 Cov.: 33 AF XY: 0.0924 AC XY: 6877 AN XY: 74448

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.0435

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0802

Gnomad4 FIN AF: 0.00292

Gnomad4 NFE AF: 0.0180

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0643 Hom.: 123

Bravo AF: 0.106

Asia WGS AF: 0.0640 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	23
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16969737; hg19: chr18-35681942;