2-75216947-C-T

Variant names:

• chr2-75216947-C-T
• rs11684394
• NR_168009.1:n.373-59563C>T

Variant summary

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

The NR_168009.1(TACR1-AS1):​n.373-59563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,836 control chromosomes in the GnomAD database, including 4,946 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 0.23 (4946 hom., cov: 30)
• Consequence: TACR1-AS1 NR_168009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 1 publications found

Genes affected

TACR1-AS1 (HGNC:58209):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_168009.1. 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-AS1	NR_168009.1		n.373-59563C>T		intron	N/A
	TACR1-AS1	NR_168010.1		n.367-59563C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35260 AN: 151716 Hom.: 4947 Cov.: 30

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.232 AC: 35259 AN: 151836 Hom.: 4946 Cov.: 30 AF XY: 0.231 AC XY: 17168 AN XY: 74186

African (AFR) AF: 0.0735 AC: 3045 AN: 41418

American (AMR) AF: 0.341 AC: 5205 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1220 AN: 5136

South Asian (SAS) AF: 0.195 AC: 934 AN: 4796

European-Finnish (FIN) AF: 0.233 AC: 2456 AN: 10536

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20543 AN: 67910

Other (OTH) AF: 0.257 AC: 541 AN: 2104

Alfa AF: 0.285 Hom.: 16779

Bravo AF: 0.237

Asia WGS AF: 0.227 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.59
PhyloP100		0.055

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11684394; hg19: chr2-75444073;