chr14-104980738-C-T

Variant names:

• chr14-104980738-C-T
• rs2033932

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 0.242 in 152,084 control chromosomes in the GnomAD database, including 4,701 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 0.24 (4701 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.11
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.242 AC: 36829 AN: 151966 Hom.: 4700 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.242 AC: 36855 AN: 152084 Hom.: 4701 Cov.: 33 AF XY: 0.246 AC XY: 18256 AN XY: 74342

African (AFR) AF: 0.297 AC: 12303 AN: 41490

American (AMR) AF: 0.264 AC: 4042 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1403 AN: 5154

South Asian (SAS) AF: 0.185 AC: 894 AN: 4826

European-Finnish (FIN) AF: 0.271 AC: 2865 AN: 10576

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13745 AN: 67958

Other (OTH) AF: 0.234 AC: 494 AN: 2110

Alfa AF: 0.211 Hom.: 9651

Bravo AF: 0.240

Asia WGS AF: 0.221 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.016
DANN	Benign	0.71
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs2033932; hg19: chr14-105447075;