rs1943418

Variant names:

• chr18-59812296-T-C
• rs1943418

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 0.755 in 152,048 control chromosomes in the GnomAD database, including 43,425 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 0.75 (43425 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

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 (SAS) allele frequency at 95% confidence interval = 0.774 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: 0.755 AC: 114663 AN: 151930 Hom.: 43395 Cov.: 31

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.755 AC: 114748 AN: 152048 Hom.: 43425 Cov.: 31 AF XY: 0.753 AC XY: 55999 AN XY: 74334

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.754

Alfa AF: 0.771 Hom.: 6295

Bravo AF: 0.747

Asia WGS AF: 0.761 AC: 2647 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	0.079
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1943418; hg19: chr18-57479528;