18-74037957-T-C

Variant names:

• chr18-74037957-T-C
• rs1943940

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 0.425 in 151,356 control chromosomes in the GnomAD database, including 13,916 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 0.42 (13916 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64268 AN: 151236 Hom.: 13909 Cov.: 29

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.425 AC: 64307 AN: 151356 Hom.: 13916 Cov.: 29 AF XY: 0.428 AC XY: 31626 AN XY: 73944

African (AFR) AF: 0.352 AC: 14509 AN: 41190

American (AMR) AF: 0.489 AC: 7442 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3464

East Asian (EAS) AF: 0.496 AC: 2522 AN: 5082

South Asian (SAS) AF: 0.458 AC: 2190 AN: 4778

European-Finnish (FIN) AF: 0.430 AC: 4512 AN: 10502

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30263 AN: 67818

Other (OTH) AF: 0.417 AC: 874 AN: 2094

Alfa AF: 0.436 Hom.: 21329

Bravo AF: 0.426

Asia WGS AF: 0.501 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.42
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs1943940; hg19: chr18-71705192;