rs1782145

Variant names:

• chr14-41261173-C-T
• rs1782145

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 0.764 in 152,114 control chromosomes in the GnomAD database, including 44,680 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 0.76 (44680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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: 0.764 AC: 116149 AN: 151996 Hom.: 44614 Cov.: 32

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.764 AC: 116275 AN: 152114 Hom.: 44680 Cov.: 32 AF XY: 0.764 AC XY: 56793 AN XY: 74342

African (AFR) AF: 0.836 AC: 34697 AN: 41490

American (AMR) AF: 0.787 AC: 12038 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2713 AN: 3472

East Asian (EAS) AF: 0.803 AC: 4152 AN: 5172

South Asian (SAS) AF: 0.661 AC: 3183 AN: 4816

European-Finnish (FIN) AF: 0.685 AC: 7234 AN: 10562

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49724 AN: 67998

Other (OTH) AF: 0.781 AC: 1646 AN: 2108

Alfa AF: 0.763 Hom.: 5741

Bravo AF: 0.776

Asia WGS AF: 0.750 AC: 2607 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.77
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1782145; hg19: chr14-41730376;