14-24341164-T-C

Variant names:

• chr14-24341164-T-C
• rs3212243

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 0.2 in 152,132 control chromosomes in the GnomAD database, including 3,885 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 0.20 (3885 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 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: 0.200 AC: 30418 AN: 152014 Hom.: 3873 Cov.: 33

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.200 AC: 30444 AN: 152132 Hom.: 3885 Cov.: 33 AF XY: 0.201 AC XY: 14924 AN XY: 74376

African (AFR) AF: 0.0504 AC: 2094 AN: 41512

American (AMR) AF: 0.330 AC: 5051 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1259 AN: 5174

South Asian (SAS) AF: 0.254 AC: 1226 AN: 4826

European-Finnish (FIN) AF: 0.205 AC: 2169 AN: 10584

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17416 AN: 67972

Other (OTH) AF: 0.225 AC: 473 AN: 2106

Alfa AF: 0.237 Hom.: 14554

Bravo AF: 0.204

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.5
DANN	Benign	0.79
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs3212243; hg19: chr14-24810370;