10-69410159-C-G

Variant names:

• chr10-69410159-C-G
• rs4644560
• NM_001057.3:c.588-1084G>C

Variant summary

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

The NM_001057.3(TACR2):​c.588-1084G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,214 control chromosomes in the GnomAD database, including 26,007 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 0.58 (26007 hom., cov: 28)
• Consequence: TACR2 NM_001057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 4 publications found

Genes affected

TACR2 (HGNC:11527): (tachykinin receptor 2) This gene belongs to a family of genes that function as receptors for tachykinins. Receptor affinities are specified by variations in the 5'-end of the sequence. The receptors belonging to this family are characterized by interactions with G proteins and 7 hydrophobic transmembrane regions. This gene encodes the receptor for the tachykinin neuropeptide substance K, also referred to as neurokinin A. [provided by RefSeq, Jul 2008]

ENSG00000299486 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR2	NM_001057.3	c.588-1084G>C		intron_variant	Intron 2 of 4	ENST00000373306.5	NP_001048.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR2	ENST00000373306.5	c.588-1084G>C		intron_variant	Intron 2 of 4	1	NM_001057.3	ENSP00000362403.4
ENSG00000299486	ENST00000763854.1	n.84+3297C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87255 AN: 151098 Hom.: 25968 Cov.: 28

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.578 AC: 87357 AN: 151214 Hom.: 26007 Cov.: 28 AF XY: 0.573 AC XY: 42314 AN XY: 73816

African (AFR) AF: 0.690 AC: 28406 AN: 41178

American (AMR) AF: 0.496 AC: 7544 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2264 AN: 3468

East Asian (EAS) AF: 0.310 AC: 1583 AN: 5106

South Asian (SAS) AF: 0.700 AC: 3361 AN: 4804

European-Finnish (FIN) AF: 0.497 AC: 5150 AN: 10358

Middle Eastern (MID) AF: 0.628 AC: 182 AN: 290

European-Non Finnish (NFE) AF: 0.547 AC: 37067 AN: 67800

Other (OTH) AF: 0.566 AC: 1190 AN: 2104

Alfa AF: 0.389 Hom.: 916

Bravo AF: 0.579

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.44
PhyloP100		0.30
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: rs4644560; hg19: chr10-71169915;