chr2-75049135-G-T

Variant names:

• chr2-75049135-G-T
• rs62148938
• NM_001058.4:c.*297C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001058.4(TACR1):​c.*297C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000506 in 217,478 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: 33)
  • Exomes 𝑓: 0.000051 (0 hom.)
• Consequence: TACR1 NM_001058.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 1 publications found

Genes affected

TACR1 (HGNC:11526): (tachykinin receptor 1) This gene belongs to a gene family of tachykinin receptors. These tachykinin receptors are characterized by interactions with G proteins and contain seven hydrophobic transmembrane regions. This gene encodes the receptor for the tachykinin substance P, also referred to as neurokinin 1. The encoded protein is also involved in the mediation of phosphatidylinositol metabolism of substance P. [provided by RefSeq, Sep 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001058.4. 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
	TACR1	NM_001058.4	MANE Select	c.*297C>A		3_prime_UTR	Exon 5 of 5	NP_001049.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	ENST00000305249.10	TSL:1 MANE Select	c.*297C>A		3_prime_UTR	Exon 5 of 5	ENSP00000303522.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000506 AC: 11 AN: 217478 Hom.: 0 Cov.: 0 AF XY: 0.0000452 AC XY: 5 AN XY: 110622

African (AFR) AF: 0.00 AC: 0 AN: 7610

American (AMR) AF: 0.00 AC: 0 AN: 8178

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7624

East Asian (EAS) AF: 0.00 AC: 0 AN: 15878

South Asian (SAS) AF: 0.000297 AC: 4 AN: 13464

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 13924

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1102

European-Non Finnish (NFE) AF: 0.0000367 AC: 5 AN: 136106

Other (OTH) AF: 0.000147 AC: 2 AN: 13592

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.76
PhyloP100		0.33

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: rs62148938; hg19: chr2-75276262;