14-97996820-T-C

Variant names:

• chr14-97996820-T-C
• rs7140601

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 0.37 in 151,992 control chromosomes in the GnomAD database, including 13,388 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 0.37 (13388 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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: 0.370 AC: 56130 AN: 151874 Hom.: 13348 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.370 AC: 56231 AN: 151992 Hom.: 13388 Cov.: 32 AF XY: 0.378 AC XY: 28046 AN XY: 74266

African (AFR) AF: 0.662 AC: 27446 AN: 41436

American (AMR) AF: 0.311 AC: 4744 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3468

East Asian (EAS) AF: 0.534 AC: 2753 AN: 5158

South Asian (SAS) AF: 0.441 AC: 2121 AN: 4812

European-Finnish (FIN) AF: 0.329 AC: 3477 AN: 10558

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 14058 AN: 67986

Other (OTH) AF: 0.338 AC: 715 AN: 2116

Alfa AF: 0.266 Hom.: 15451

Bravo AF: 0.377

Asia WGS AF: 0.518 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.058
DANN	Benign	0.71
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7140601; hg19: chr14-98463157;