rs6997

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-49416401-C-G
• chr3-49416401-C-T

Variant summary

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

The NM_022171.3(TCTA):​c.*1539C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000911 in 109,726 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000091 (0 hom.)
• Consequence: TCTA NM_022171.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 0 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: 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=-0.81).

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>G		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>G		3_prime_UTR	Exon 3 of 3	ENSP00000273590.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000911 AC: 1 AN: 109726 Hom.: 0 Cov.: 0 AF XY: 0.0000171 AC XY: 1 AN XY: 58524

African (AFR) AF: 0.00 AC: 0 AN: 3980

American (AMR) AF: 0.00 AC: 0 AN: 4944

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2482

East Asian (EAS) AF: 0.00 AC: 0 AN: 5718

South Asian (SAS) AF: 0.0000525 AC: 1 AN: 19064

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4654

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 414

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 63026

Other (OTH) AF: 0.00 AC: 0 AN: 5444

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		-0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;