7-97732472-C-T

Variant names:

• chr7-97732472-C-T
• rs2072100
• NM_003182.3:c.-9-132C>T

Variant summary

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

The NM_003182.3(TAC1):​c.-9-132C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,053,232 control chromosomes in the GnomAD database, including 142,997 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 0.55 (23786 hom., cov: 31)
  • Exomes 𝑓: 0.51 (119211 hom.)
• Consequence: TAC1 NM_003182.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 17 publications found

Genes affected

TAC1 (HGNC:11517): (tachykinin precursor 1) This gene encodes four products of the tachykinin peptide hormone family, substance P and neurokinin A, as well as the related peptides, neuropeptide K and neuropeptide gamma. These hormones are thought to function as neurotransmitters which interact with nerve receptors and smooth muscle cells. They are known to induce behavioral responses and function as vasodilators and secretagogues. Substance P is an antimicrobial peptide with antibacterial and antifungal properties. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003182.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAC1	NM_003182.3	MANE Select	c.-9-132C>T		intron	N/A	NP_003173.1	P20366-1
	TAC1	NM_013997.3		c.-9-132C>T		intron	N/A	NP_054703.1	P20366-3
	TAC1	NM_013996.3		c.-9-132C>T		intron	N/A	NP_054702.1	P20366-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAC1	ENST00000319273.10	TSL:1 MANE Select	c.-9-132C>T		intron	N/A	ENSP00000321106.5	P20366-1
	TAC1	ENST00000926836.1		c.-10+10C>T		intron	N/A	ENSP00000596895.1
	TAC1	ENST00000962701.1		c.-10+108C>T		intron	N/A	ENSP00000632760.1

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83766 AN: 151826 Hom.: 23755 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.531

GnomAD4 exome AF: 0.509 AC: 458470 AN: 901286 Hom.: 119211 AF XY: 0.508 AC XY: 234411 AN XY: 461202

African (AFR) AF: 0.697 AC: 15208 AN: 21830

American (AMR) AF: 0.393 AC: 13322 AN: 33926

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 9193 AN: 17904

East Asian (EAS) AF: 0.356 AC: 13033 AN: 36580

South Asian (SAS) AF: 0.463 AC: 28843 AN: 62302

European-Finnish (FIN) AF: 0.537 AC: 20023 AN: 37320

Middle Eastern (MID) AF: 0.471 AC: 2090 AN: 4438

European-Non Finnish (NFE) AF: 0.520 AC: 335564 AN: 645678

Other (OTH) AF: 0.513 AC: 21194 AN: 41308

GnomAD4 genome AF: 0.552 AC: 83858 AN: 151946 Hom.: 23786 Cov.: 31 AF XY: 0.549 AC XY: 40766 AN XY: 74272

African (AFR) AF: 0.687 AC: 28477 AN: 41454

American (AMR) AF: 0.439 AC: 6718 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1733 AN: 3466

East Asian (EAS) AF: 0.378 AC: 1947 AN: 5150

South Asian (SAS) AF: 0.478 AC: 2295 AN: 4804

European-Finnish (FIN) AF: 0.527 AC: 5558 AN: 10550

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35297 AN: 67920

Other (OTH) AF: 0.532 AC: 1122 AN: 2110

Alfa AF: 0.519 Hom.: 34345

Bravo AF: 0.550

Asia WGS AF: 0.442 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.2
DANN	Benign	0.89
PhyloP100		0.16
PromoterAI		0.0038	Neutral
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: rs2072100; hg19: chr7-97361784;