2-75200118-G-A

Variant names:

• chr2-75200118-G-A
• rs13384011
• NR_168009.1:n.372+43803G>A

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+43803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0626 in 152,322 control chromosomes in the GnomAD database, including 338 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 0.063 (338 hom., cov: 33)
• Consequence: TACR1-AS1 NR_168009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834
• 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.079 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.372+43803G>A		intron	N/A
	TACR1-AS1	NR_168010.1		n.366+43803G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9528 AN: 152204 Hom.: 339 Cov.: 33

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.00829

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0808

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0626 AC: 9531 AN: 152322 Hom.: 338 Cov.: 33 AF XY: 0.0602 AC XY: 4485 AN XY: 74480

African (AFR) AF: 0.0568 AC: 2362 AN: 41582

American (AMR) AF: 0.0398 AC: 609 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0351 AC: 122 AN: 3472

East Asian (EAS) AF: 0.00831 AC: 43 AN: 5172

South Asian (SAS) AF: 0.0323 AC: 156 AN: 4828

European-Finnish (FIN) AF: 0.0533 AC: 566 AN: 10620

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0808 AC: 5497 AN: 68016

Other (OTH) AF: 0.0633 AC: 134 AN: 2116

Alfa AF: 0.0573 Hom.: 111

Bravo AF: 0.0622

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.7
DANN	Benign	0.58
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs13384011; hg19: chr2-75427244;