18-41852713-C-T

Variant names:

• chr18-41852713-C-T
• rs768343

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 0.545 in 151,894 control chromosomes in the GnomAD database, including 23,566 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 0.55 (23566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 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: 0.546 AC: 82799 AN: 151778 Hom.: 23571 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.545 AC: 82802 AN: 151894 Hom.: 23566 Cov.: 32 AF XY: 0.539 AC XY: 39987 AN XY: 74216

African (AFR) AF: 0.396 AC: 16409 AN: 41402

American (AMR) AF: 0.453 AC: 6922 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3470

East Asian (EAS) AF: 0.397 AC: 2047 AN: 5156

South Asian (SAS) AF: 0.523 AC: 2516 AN: 4814

European-Finnish (FIN) AF: 0.639 AC: 6754 AN: 10568

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44178 AN: 67900

Other (OTH) AF: 0.544 AC: 1151 AN: 2116

Alfa AF: 0.496 Hom.: 2519

Bravo AF: 0.518

Asia WGS AF: 0.453 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs768343; hg19: chr18-39432678;