rs1154140

Variant names:

• chr14-40917801-G-A
• rs1154140

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 0.634 in 151,996 control chromosomes in the GnomAD database, including 30,853 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 0.63 (30853 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 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: 0.634 AC: 96318 AN: 151878 Hom.: 30822 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.634 AC: 96390 AN: 151996 Hom.: 30853 Cov.: 32 AF XY: 0.629 AC XY: 46757 AN XY: 74290

African (AFR) AF: 0.571 AC: 23674 AN: 41442

American (AMR) AF: 0.636 AC: 9715 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2507 AN: 3470

East Asian (EAS) AF: 0.477 AC: 2457 AN: 5148

South Asian (SAS) AF: 0.585 AC: 2820 AN: 4820

European-Finnish (FIN) AF: 0.623 AC: 6585 AN: 10576

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46453 AN: 67966

Other (OTH) AF: 0.640 AC: 1345 AN: 2102

Alfa AF: 0.665 Hom.: 16567

Bravo AF: 0.631

Asia WGS AF: 0.512 AC: 1782 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	0.60
DANN	Benign	0.43
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs1154140; hg19: chr14-41387006;