chr14-97369307-A-T

Variant names:

• chr14-97369307-A-T
• rs17095290

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 0.0505 in 151,856 control chromosomes in the GnomAD database, including 636 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 0.050 (636 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.225 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: 0.0505 AC: 7657 AN: 151738 Hom.: 634 Cov.: 31

Gnomad AFR AF: 0.0579

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.00218

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0663

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

GnomAD4 genome AF: 0.0505 AC: 7668 AN: 151856 Hom.: 636 Cov.: 31 AF XY: 0.0541 AC XY: 4014 AN XY: 74186

African (AFR) AF: 0.0578 AC: 2390 AN: 41330

American (AMR) AF: 0.232 AC: 3528 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3470

East Asian (EAS) AF: 0.118 AC: 608 AN: 5156

South Asian (SAS) AF: 0.0247 AC: 119 AN: 4816

European-Finnish (FIN) AF: 0.00218 AC: 23 AN: 10546

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0111 AC: 758 AN: 67994

Other (OTH) AF: 0.0657 AC: 138 AN: 2102

Alfa AF: 0.0295 Hom.: 32

Bravo AF: 0.0706

Asia WGS AF: 0.0670 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.77
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs17095290; hg19: chr14-97835644;