chr14-95605368-T-C

Variant names:

• chr14-95605368-T-C
• rs911669

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.389 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

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.394

Alfa AF: 0.334 Hom.: 14093

Bravo AF: 0.398

Asia WGS AF: 0.576 AC: 2002 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	1.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

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