rs1243679

Variant names:

• chr14-20625574-A-G
• rs1243679
• unassigned_transcript_2170:c.*123A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000000000(TRL-TAG2-1):​c.*123A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,164 control chromosomes in the GnomAD database, including 1,535 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 0.11 (1535 hom., cov: 32)
• Consequence: TRL-TAG2-1 ENST00000000000 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 3 publications found

Genes affected

TRL-TAG2-1 (HGNC:34713):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRL-TAG2-1	unassigned_transcript_2170	c.*123A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16857 AN: 152046 Hom.: 1531 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.0953

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0421

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.111 AC: 16905 AN: 152164 Hom.: 1535 Cov.: 32 AF XY: 0.112 AC XY: 8317 AN XY: 74410

African (AFR) AF: 0.238 AC: 9858 AN: 41450

American (AMR) AF: 0.0953 AC: 1458 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3472

East Asian (EAS) AF: 0.189 AC: 981 AN: 5182

South Asian (SAS) AF: 0.216 AC: 1040 AN: 4820

European-Finnish (FIN) AF: 0.0265 AC: 281 AN: 10614

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0421 AC: 2865 AN: 68012

Other (OTH) AF: 0.0917 AC: 194 AN: 2116

Alfa AF: 0.0676 Hom.: 2341

Bravo AF: 0.121

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	0.10
DANN	Benign	0.23
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1243679; hg19: chr14-21093733;