rs1943418

chr18-59812296-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;