3-49416401-C-T

Variant names:

• chr3-49416401-C-T
• rs6997
• NM_022171.3:c.*1539C>T

Variant summary

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

The NM_022171.3(TCTA):​c.*1539C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 261,562 control chromosomes in the GnomAD database, including 11,879 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 0.30 (7228 hom., cov: 32)
  • Exomes 𝑓: 0.27 (4651 hom.)
• Consequence: TCTA NM_022171.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 47 publications found

Genes affected

TCTA (HGNC:11692): (T cell leukemia translocation altered) Involved in negative regulation of osteoclast differentiation and osteoclast fusion. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022171.3. 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
	TCTA	NM_022171.3	MANE Select	c.*1539C>T		3_prime_UTR	Exon 3 of 3	NP_071503.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCTA	ENST00000273590.4	TSL:1 MANE Select	c.*1539C>T		3_prime_UTR	Exon 3 of 3	ENSP00000273590.3

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45243 AN: 152072 Hom.: 7220 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.0586

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.273 AC: 29831 AN: 109372 Hom.: 4651 Cov.: 0 AF XY: 0.267 AC XY: 15568 AN XY: 58336

African (AFR) AF: 0.273 AC: 1084 AN: 3970

American (AMR) AF: 0.179 AC: 884 AN: 4936

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1088 AN: 2472

East Asian (EAS) AF: 0.0504 AC: 288 AN: 5718

South Asian (SAS) AF: 0.228 AC: 4341 AN: 19000

European-Finnish (FIN) AF: 0.428 AC: 1982 AN: 4628

Middle Eastern (MID) AF: 0.326 AC: 135 AN: 414

European-Non Finnish (NFE) AF: 0.292 AC: 18354 AN: 62808

Other (OTH) AF: 0.309 AC: 1675 AN: 5426

GnomAD4 genome AF: 0.297 AC: 45274 AN: 152190 Hom.: 7228 Cov.: 32 AF XY: 0.300 AC XY: 22285 AN XY: 74400

African (AFR) AF: 0.293 AC: 12161 AN: 41496

American (AMR) AF: 0.220 AC: 3360 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1600 AN: 3470

East Asian (EAS) AF: 0.0589 AC: 306 AN: 5194

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4830

European-Finnish (FIN) AF: 0.472 AC: 4998 AN: 10592

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20845 AN: 68004

Other (OTH) AF: 0.298 AC: 628 AN: 2110

Alfa AF: 0.300 Hom.: 8749

Bravo AF: 0.277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

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: rs6997; hg19: chr3-49453834;