14-41246365-T-C

Variant names:

• chr14-41246365-T-C
• rs1782134

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 0.757 in 151,936 control chromosomes in the GnomAD database, including 43,788 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 (43788 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.757 AC: 114878 AN: 151816 Hom.: 43730 Cov.: 33

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.757 AC: 114998 AN: 151936 Hom.: 43788 Cov.: 33 AF XY: 0.756 AC XY: 56101 AN XY: 74246

African (AFR) AF: 0.828 AC: 34383 AN: 41512

American (AMR) AF: 0.786 AC: 12002 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2728 AN: 3466

East Asian (EAS) AF: 0.708 AC: 3663 AN: 5174

South Asian (SAS) AF: 0.652 AC: 3148 AN: 4826

European-Finnish (FIN) AF: 0.679 AC: 7181 AN: 10570

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49369 AN: 67800

Other (OTH) AF: 0.776 AC: 1635 AN: 2108

Alfa AF: 0.757 Hom.: 6280

Bravo AF: 0.768

Asia WGS AF: 0.707 AC: 2453 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.70
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1782134; hg19: chr14-41715568;