14-94329847-A-T

Variant names:

• chr14-94329847-A-T
• rs61280460

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 0.179 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.0542 AC: 2252 AN: 41552

American (AMR) AF: 0.274 AC: 4191 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2384 AN: 5170

South Asian (SAS) AF: 0.130 AC: 627 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2456 AN: 10570

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14313 AN: 68004

Other (OTH) AF: 0.190 AC: 403 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.73
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs61280460; hg19: chr14-94796184;