14-92757645-C-T

Variant names:

• chr14-92757645-C-T
• rs7160685

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 0.287 in 152,030 control chromosomes in the GnomAD database, including 6,930 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 0.29 (6930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 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: 0.288 AC: 43701 AN: 151912 Hom.: 6927 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.287 AC: 43702 AN: 152030 Hom.: 6930 Cov.: 32 AF XY: 0.293 AC XY: 21760 AN XY: 74296

African (AFR) AF: 0.160 AC: 6617 AN: 41450

American (AMR) AF: 0.358 AC: 5466 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1098 AN: 3468

East Asian (EAS) AF: 0.468 AC: 2425 AN: 5182

South Asian (SAS) AF: 0.371 AC: 1785 AN: 4814

European-Finnish (FIN) AF: 0.314 AC: 3314 AN: 10556

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22038 AN: 67962

Other (OTH) AF: 0.277 AC: 585 AN: 2110

Alfa AF: 0.316 Hom.: 11842

Bravo AF: 0.286

Asia WGS AF: 0.377 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.72
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs7160685; hg19: chr14-93223990;