rs1474477

Variant names:

• chr14-22317783-C-T
• rs1474477

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 0.15 in 149,900 control chromosomes in the GnomAD database, including 1,743 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 0.15 (1743 hom., cov: 25)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22317783C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRD-AS1	ENST00000656379.1	n.270+83261G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22402 AN: 149782 Hom.: 1740 Cov.: 25

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.150 AC: 22418 AN: 149900 Hom.: 1743 Cov.: 25 AF XY: 0.151 AC XY: 11020 AN XY: 73134

African (AFR) AF: 0.147 AC: 5968 AN: 40622

American (AMR) AF: 0.202 AC: 3003 AN: 14882

Ashkenazi Jewish (ASJ) AF: 0.0954 AC: 330 AN: 3458

East Asian (EAS) AF: 0.136 AC: 699 AN: 5130

South Asian (SAS) AF: 0.177 AC: 844 AN: 4762

European-Finnish (FIN) AF: 0.128 AC: 1295 AN: 10124

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9759 AN: 67630

Other (OTH) AF: 0.154 AC: 321 AN: 2088

Alfa AF: 0.149 Hom.: 1322

Bravo AF: 0.159

Asia WGS AF: 0.162 AC: 563 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.62
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1474477; hg19: chr14-22786215;