rs1741240

Variant names:

• chr14-94895704-C-G
• rs1741240

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 0.572 in 152,044 control chromosomes in the GnomAD database, including 25,793 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 0.57 (25793 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 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: 0.572 AC: 86915 AN: 151926 Hom.: 25761 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.572 AC: 87004 AN: 152044 Hom.: 25793 Cov.: 32 AF XY: 0.568 AC XY: 42186 AN XY: 74314

African (AFR) AF: 0.662 AC: 27449 AN: 41478

American (AMR) AF: 0.435 AC: 6650 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1995 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1309 AN: 5152

South Asian (SAS) AF: 0.351 AC: 1692 AN: 4814

European-Finnish (FIN) AF: 0.643 AC: 6789 AN: 10566

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39277 AN: 67968

Other (OTH) AF: 0.566 AC: 1196 AN: 2112

Alfa AF: 0.588 Hom.: 3349

Bravo AF: 0.560

Asia WGS AF: 0.386 AC: 1346 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	0.77
DANN	Benign	0.33
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1741240; hg19: chr14-95362041;