18-40335525-T-C

Variant names:

• chr18-40335525-T-C
• rs2862364

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0613 in 152,082 control chromosomes in the GnomAD database, including 427 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 0.061 (427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 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: 0.0613 AC: 9310 AN: 151964 Hom.: 426 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0613 AC: 9323 AN: 152082 Hom.: 427 Cov.: 32 AF XY: 0.0620 AC XY: 4611 AN XY: 74318

African (AFR) AF: 0.126 AC: 5228 AN: 41516

American (AMR) AF: 0.0325 AC: 495 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.00519 AC: 18 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.0493 AC: 238 AN: 4830

European-Finnish (FIN) AF: 0.0655 AC: 693 AN: 10580

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0375 AC: 2548 AN: 67960

Other (OTH) AF: 0.0402 AC: 85 AN: 2112

Alfa AF: 0.0259 Hom.: 24

Bravo AF: 0.0598

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.69
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2862364; hg19: chr18-37915489;