14-69034335-G-T

Variant names:

• chr14-69034335-G-T
• rs761899

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 0.49 in 151,798 control chromosomes in the GnomAD database, including 19,339 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 0.49 (19339 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74233 AN: 151680 Hom.: 19303 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.490 AC: 74307 AN: 151798 Hom.: 19339 Cov.: 31 AF XY: 0.495 AC XY: 36699 AN XY: 74164

African (AFR) AF: 0.546 AC: 22595 AN: 41354

American (AMR) AF: 0.569 AC: 8679 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1236 AN: 3468

East Asian (EAS) AF: 0.978 AC: 5051 AN: 5166

South Asian (SAS) AF: 0.559 AC: 2678 AN: 4790

European-Finnish (FIN) AF: 0.436 AC: 4588 AN: 10522

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28002 AN: 67932

Other (OTH) AF: 0.451 AC: 946 AN: 2098

Alfa AF: 0.431 Hom.: 23672

Bravo AF: 0.507

Asia WGS AF: 0.746 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.67
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs761899; hg19: chr14-69501052;