14-20489274-T-C

Variant names:

• chr14-20489274-T-C
• rs12147450

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 0.17 in 152,196 control chromosomes in the GnomAD database, including 2,282 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 0.17 (2282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 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: 0.170 AC: 25827 AN: 152078 Hom.: 2277 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.00557

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.170 AC: 25844 AN: 152196 Hom.: 2282 Cov.: 32 AF XY: 0.167 AC XY: 12440 AN XY: 74426

African (AFR) AF: 0.157 AC: 6503 AN: 41526

American (AMR) AF: 0.153 AC: 2333 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3470

East Asian (EAS) AF: 0.00559 AC: 29 AN: 5192

South Asian (SAS) AF: 0.124 AC: 597 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1941 AN: 10580

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12540 AN: 68008

Other (OTH) AF: 0.204 AC: 432 AN: 2116

Alfa AF: 0.177 Hom.: 7444

Bravo AF: 0.169

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.8
DANN	Benign	0.71
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs12147450; hg19: chr14-20957433;