14-22331640-T-G

Variant names:

• chr14-22331640-T-G
• rs11627649

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 0.0638 in 151,216 control chromosomes in the GnomAD database, including 352 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 0.064 (352 hom., cov: 26)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0786 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRD-AS1	ENST00000656379.1		n.270+69404A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9641 AN: 151098 Hom.: 350 Cov.: 26

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0540

Gnomad ASJ AF: 0.0748

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.0653

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

GnomAD4 genome AF: 0.0638 AC: 9648 AN: 151216 Hom.: 352 Cov.: 26 AF XY: 0.0628 AC XY: 4640 AN XY: 73904

African (AFR) AF: 0.0495 AC: 2035 AN: 41112

American (AMR) AF: 0.0539 AC: 811 AN: 15040

Ashkenazi Jewish (ASJ) AF: 0.0748 AC: 259 AN: 3464

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5174

South Asian (SAS) AF: 0.0613 AC: 294 AN: 4796

European-Finnish (FIN) AF: 0.0449 AC: 471 AN: 10498

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0804 AC: 5454 AN: 67842

Other (OTH) AF: 0.0641 AC: 134 AN: 2090

Alfa AF: 0.0650 Hom.: 210

Bravo AF: 0.0633

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.72
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11627649; hg19: chr14-22800070;