chr1-23381148-T-C

Variant names:

• chr1-23381148-T-C
• rs3192564
• NM_003196.3:c.*318A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003196.3(TCEA3):​c.*318A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TCEA3 NM_003196.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 publications found

Genes affected

TCEA3 (HGNC:11615): (transcription elongation factor A3) Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription, DNA-templated and transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCEA3	NM_003196.3	c.*318A>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000450454.7	NP_003187.1
TCEA3	XM_011542053.4	c.*327A>G		downstream_gene_variant			XP_011540355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCEA3	ENST00000450454.7	c.*318A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_003196.3	ENSP00000406293.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 186530 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 98596

African (AFR) AF: 0.00 AC: 0 AN: 4924

American (AMR) AF: 0.00 AC: 0 AN: 6486

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5982

East Asian (EAS) AF: 0.00 AC: 0 AN: 11200

South Asian (SAS) AF: 0.00 AC: 0 AN: 18838

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10234

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 826

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 117096

Other (OTH) AF: 0.00 AC: 0 AN: 10944

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.29
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3192564; hg19: chr1-23707641;