NR_168009.1:n.372+46447A>G

Variant names:

• chr2-75202762-A-G
• rs59099335
• NR_168009.1:n.372+46447A>G

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.372+46447A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,184 control chromosomes in the GnomAD database, including 2,290 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 0.15 (2290 hom., cov: 33)
• Consequence: TACR1-AS1 NR_168009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1-AS1	NR_168009.1		n.372+46447A>G		intron	N/A
	TACR1-AS1	NR_168010.1		n.366+46447A>G		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22883 AN: 152066 Hom.: 2292 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.151 AC: 22907 AN: 152184 Hom.: 2290 Cov.: 33 AF XY: 0.153 AC XY: 11400 AN XY: 74422

African (AFR) AF: 0.264 AC: 10947 AN: 41494

American (AMR) AF: 0.131 AC: 1998 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0669 AC: 232 AN: 3470

East Asian (EAS) AF: 0.285 AC: 1476 AN: 5176

South Asian (SAS) AF: 0.240 AC: 1157 AN: 4822

European-Finnish (FIN) AF: 0.102 AC: 1080 AN: 10602

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0826 AC: 5618 AN: 68008

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.115 Hom.: 302

Bravo AF: 0.158

Asia WGS AF: 0.250 AC: 865 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs59099335; hg19: chr2-75429888;