2-75202102-A-G

Variant names:

• chr2-75202102-A-G
• rs1477157
• NR_168009.1:n.372+45787A>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+45787A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,128 control chromosomes in the GnomAD database, including 26,358 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 0.56 (26358 hom., cov: 33)
• Consequence: TACR1-AS1 NR_168009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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+45787A>G		intron	N/A
	TACR1-AS1	NR_168010.1		n.366+45787A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85588 AN: 152010 Hom.: 26318 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.563 AC: 85692 AN: 152128 Hom.: 26358 Cov.: 33 AF XY: 0.555 AC XY: 41289 AN XY: 74372

African (AFR) AF: 0.837 AC: 34741 AN: 41530

American (AMR) AF: 0.490 AC: 7488 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2122 AN: 5178

South Asian (SAS) AF: 0.403 AC: 1937 AN: 4812

European-Finnish (FIN) AF: 0.414 AC: 4376 AN: 10560

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32178 AN: 67978

Other (OTH) AF: 0.538 AC: 1135 AN: 2110

Alfa AF: 0.496 Hom.: 74101

Bravo AF: 0.584

Asia WGS AF: 0.447 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.49
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1477157; hg19: chr2-75429228;