14-95605368-T-C

Variant names:

• chr14-95605368-T-C
• rs911669

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 0.389 in 152,000 control chromosomes in the GnomAD database, including 12,166 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 0.39 (12166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 8 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 = 0.541 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59132 AN: 151880 Hom.: 12143 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.389 AC: 59189 AN: 152000 Hom.: 12166 Cov.: 32 AF XY: 0.390 AC XY: 28939 AN XY: 74268

African (AFR) AF: 0.500 AC: 20727 AN: 41450

American (AMR) AF: 0.347 AC: 5294 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3468

East Asian (EAS) AF: 0.558 AC: 2867 AN: 5134

South Asian (SAS) AF: 0.541 AC: 2598 AN: 4806

European-Finnish (FIN) AF: 0.299 AC: 3172 AN: 10594

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22050 AN: 67962

Other (OTH) AF: 0.394 AC: 830 AN: 2106

Alfa AF: 0.350 Hom.: 25596

Bravo AF: 0.398

Asia WGS AF: 0.576 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs911669; hg19: chr14-96071705; COSMIC: COSV58121705;