14-94329847-A-T

Position:

• chr14-94329847-A-T

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 0.179 in 152,186 control chromosomes in the GnomAD database, including 3,208 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 0.18 (3208 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27269 AN: 152070 Hom.: 3206 Cov.: 33

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.179 AC: 27272 AN: 152186 Hom.: 3208 Cov.: 33 AF XY: 0.184 AC XY: 13681 AN XY: 74376

Gnomad4 AFR AF: 0.0542

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.190

Alfa AF: 0.107 Hom.: 200

Bravo AF: 0.185

Asia WGS AF: 0.279 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61280460; hg19: chr14-94796184;