XR_946382.3:n.2646A>G

Variant names:

• chr10-122450168-T-C
• rs11200630
• XR_946382.3:n.2646A>G

Variant summary

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

The XR_946382.3(HTRA1-AS1):​n.2646A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,166 control chromosomes in the GnomAD database, including 3,966 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 0.22 (3966 hom., cov: 32)
• Consequence: HTRA1-AS1 XR_946382.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 10 publications found

Genes affected

HTRA1-AS1 (HGNC:58122):

ENSG00000305527 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650300.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285955	ENST00000650300.1		n.1852+8327A>G		intron	N/A
	ENSG00000305527	ENST00000811549.1		n.243-413T>C		intron	N/A
	ENSG00000285955	ENST00000811415.1		n.*26A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33787 AN: 152048 Hom.: 3960 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.222 AC: 33820 AN: 152166 Hom.: 3966 Cov.: 32 AF XY: 0.225 AC XY: 16739 AN XY: 74370

African (AFR) AF: 0.185 AC: 7665 AN: 41524

American (AMR) AF: 0.232 AC: 3555 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2129 AN: 5166

South Asian (SAS) AF: 0.318 AC: 1530 AN: 4816

European-Finnish (FIN) AF: 0.235 AC: 2484 AN: 10582

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14934 AN: 68006

Other (OTH) AF: 0.227 AC: 477 AN: 2104

Alfa AF: 0.181 Hom.: 652

Bravo AF: 0.223

Asia WGS AF: 0.363 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.46
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11200630; hg19: chr10-124209684;