rs1918942

Variant names:

• chr12-40602159-T-C
• rs1918942

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 0.386 in 151,836 control chromosomes in the GnomAD database, including 11,963 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 0.39 (11963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.864
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 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: 0.385 AC: 58481 AN: 151720 Hom.: 11936 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.386 AC: 58556 AN: 151836 Hom.: 11963 Cov.: 32 AF XY: 0.386 AC XY: 28675 AN XY: 74218

African (AFR) AF: 0.535 AC: 22165 AN: 41430

American (AMR) AF: 0.287 AC: 4366 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1314 AN: 5172

South Asian (SAS) AF: 0.336 AC: 1617 AN: 4818

European-Finnish (FIN) AF: 0.410 AC: 4335 AN: 10570

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22734 AN: 67844

Other (OTH) AF: 0.349 AC: 736 AN: 2110

Alfa AF: 0.345 Hom.: 36474

Bravo AF: 0.380

Asia WGS AF: 0.288 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.3
DANN	Benign	0.41
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs1918942; hg19: chr12-40995961;