chr10-69411010-G-C

Position:

• chr10-69411010-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001057.3(TACR2):​c.588-1935C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,966 control chromosomes in the GnomAD database, including 17,576 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 0.47 (17576 hom., cov: 32)
• Consequence: TACR2 NM_001057.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACR2	NM_001057.3	c.588-1935C>G		intron_variant		ENST00000373306.5	NP_001048.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACR2	ENST00000373306.5	c.588-1935C>G		intron_variant		1	NM_001057.3	ENSP00000362403.4

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70699 AN: 151848 Hom.: 17544 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.466 AC: 70787 AN: 151966 Hom.: 17576 Cov.: 32 AF XY: 0.458 AC XY: 34025 AN XY: 74264

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.460

Alfa AF: 0.442 Hom.: 1898

Bravo AF: 0.477

Asia WGS AF: 0.373 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs10823365; hg19: chr10-71170766;