NR_168009.1:n.372+43462G>C

Variant names:

• chr2-75199777-G-C
• rs10210648
• NR_168009.1:n.372+43462G>C

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+43462G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0615 in 152,430 control chromosomes in the GnomAD database, including 333 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 0.062 (333 hom., cov: 33)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: TACR1-AS1 NR_168009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0791 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+43462G>C		intron	N/A
	TACR1-AS1	NR_168010.1		n.366+43462G>C		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: 0.0615 AC: 9363 AN: 152184 Hom.: 334 Cov.: 33

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.00811

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0809

Gnomad OTH AF: 0.0616

GnomAD4 exome AF: 0.0625 AC: 8 AN: 128 Hom.: 0 AF XY: 0.0732 AC XY: 6 AN XY: 82

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0761 AC: 7 AN: 92

Other (OTH) AF: 0.0833 AC: 1 AN: 12

GnomAD4 genome AF: 0.0615 AC: 9367 AN: 152302 Hom.: 333 Cov.: 33 AF XY: 0.0592 AC XY: 4408 AN XY: 74484

African (AFR) AF: 0.0530 AC: 2202 AN: 41572

American (AMR) AF: 0.0395 AC: 605 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3470

East Asian (EAS) AF: 0.00813 AC: 42 AN: 5168

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: 0.0809 AC: 5501 AN: 68014

Other (OTH) AF: 0.0619 AC: 131 AN: 2116

Alfa AF: 0.0267 Hom.: 19

Bravo AF: 0.0609

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.0
DANN	Benign	0.39
PhyloP100		-0.21
PromoterAI		0.080	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10210648; hg19: chr2-75426903;