rs10490308

Variant names:

• chr2-75255249-A-C
• rs10490308
• ENST00000821460.1:n.470+15553A>C

Variant summary

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

The ENST00000821460.1(ENSG00000306831):​n.470+15553A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,210 control chromosomes in the GnomAD database, including 857 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 0.10 (857 hom., cov: 32)
• Consequence: ENSG00000306831 ENST00000821460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 6 publications found

Genes affected

ENSG00000306831 (HGNC:):

TACR1-AS1 (HGNC:58209):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1-AS1	NR_168009.1	n.373-21261A>C		intron_variant	Intron 2 of 3
TACR1-AS1	NR_168010.1	n.367-21261A>C		intron_variant	Intron 2 of 3
LOC107985900	XR_001739546.2	n.29565-17387T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306831	ENST00000821460.1	n.470+15553A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15561 AN: 152092 Hom.: 856 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.0690

Gnomad EAS AF: 0.00808

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.102 AC: 15572 AN: 152210 Hom.: 857 Cov.: 32 AF XY: 0.0998 AC XY: 7429 AN XY: 74424

African (AFR) AF: 0.108 AC: 4493 AN: 41528

American (AMR) AF: 0.0845 AC: 1293 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0690 AC: 239 AN: 3466

East Asian (EAS) AF: 0.00810 AC: 42 AN: 5186

South Asian (SAS) AF: 0.0652 AC: 315 AN: 4828

European-Finnish (FIN) AF: 0.0817 AC: 867 AN: 10606

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.117 AC: 7986 AN: 67984

Other (OTH) AF: 0.120 AC: 254 AN: 2110

Alfa AF: 0.113 Hom.: 1927

Bravo AF: 0.104

Asia WGS AF: 0.0410 AC: 141 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.77
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs10490308; hg19: chr2-75482375;