rs916048

Variant names:

• chr14-22322488-C-A
• rs916048

Your query was ambiguous. Multiple possible variants found:

• chr14-22322488-C-A
• chr14-22322488-C-G
• chr14-22322488-C-T

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 0.391 in 150,178 control chromosomes in the GnomAD database, including 11,659 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 (11659 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 10 publications found

Genes affected

TRA (HGNC:12027):

TRD-AS1 (HGNC:56197): (TRD antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656379.1. You can select a different transcript below to see updated ACMG assignments.

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
	TRD-AS1	ENST00000656379.1		n.270+78556G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 58699 AN: 150060 Hom.: 11659 Cov.: 25

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.391 AC: 58732 AN: 150178 Hom.: 11659 Cov.: 25 AF XY: 0.396 AC XY: 29047 AN XY: 73296

African (AFR) AF: 0.411 AC: 16712 AN: 40642

American (AMR) AF: 0.342 AC: 5118 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1421 AN: 3452

East Asian (EAS) AF: 0.519 AC: 2648 AN: 5106

South Asian (SAS) AF: 0.470 AC: 2241 AN: 4770

European-Finnish (FIN) AF: 0.423 AC: 4355 AN: 10296

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25046 AN: 67642

Other (OTH) AF: 0.387 AC: 812 AN: 2096

Alfa AF: 0.361 Hom.: 6300

Bravo AF: 0.384

Asia WGS AF: 0.503 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.67
DANN	Benign	0.49
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs916048; hg19: chr14-22790920;