rs11200630

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-122450168-T-C
• chr10-122450168-T-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTRA1-AS1	XR_946382.3	n.2646A>G		non_coding_transcript_exon_variant	Exon 3 of 3
HTRA1-AS1	XR_946383.3	n.2449A>G		non_coding_transcript_exon_variant	Exon 4 of 4
HTRA1-AS1	XR_946384.3	n.2373A>G		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285955	ENST00000650300.1	n.1852+8327A>G		intron_variant	Intron 2 of 2
ENSG00000305527	ENST00000811549.1	n.243-413T>C		intron_variant	Intron 1 of 1
ENSG00000285955	ENST00000811415.1	n.*26A>G		downstream_gene_variant
ENSG00000285955	ENST00000811416.1	n.*192A>G		downstream_gene_variant

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 v4.3

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;