14-97094613-C-T

Variant names:

• chr14-97094613-C-T
• rs1022590

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 0.282 in 152,098 control chromosomes in the GnomAD database, including 7,443 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 0.28 (7443 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.612 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: 0.282 AC: 42793 AN: 151980 Hom.: 7418 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.282 AC: 42873 AN: 152098 Hom.: 7443 Cov.: 33 AF XY: 0.284 AC XY: 21145 AN XY: 74352

African (AFR) AF: 0.459 AC: 19020 AN: 41462

American (AMR) AF: 0.211 AC: 3222 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3260 AN: 5178

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4822

European-Finnish (FIN) AF: 0.229 AC: 2419 AN: 10578

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12316 AN: 67996

Other (OTH) AF: 0.279 AC: 590 AN: 2112

Alfa AF: 0.213 Hom.: 17371

Bravo AF: 0.290

Asia WGS AF: 0.433 AC: 1502 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	0.74
DANN	Benign	0.59
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1022590; hg19: chr14-97560950;