rs12571363

Positions:

• chr10-122471096-C-A
• chr10-122471096-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002775.5(HTRA1):​c.472+8972C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0725 in 152,242 control chromosomes in the GnomAD database, including 498 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 0.073 (498 hom., cov: 31)
• Consequence: HTRA1 NM_002775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

HTRA1 (HGNC:9476): (HtrA serine peptidase 1) This gene encodes a member of the trypsin family of serine proteases. This protein is a secreted enzyme that is proposed to regulate the availability of insulin-like growth factors (IGFs) by cleaving IGF-binding proteins. It has also been suggested to be a regulator of cell growth. Variations in the promoter region of this gene are the cause of susceptibility to age-related macular degeneration type 7. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTRA1	NM_002775.5	c.472+8972C>A		intron_variant		ENST00000368984.8	NP_002766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTRA1	ENST00000368984.8	c.472+8972C>A		intron_variant		1	NM_002775.5	ENSP00000357980	P1
HTRA1	ENST00000648167.1	c.154+12387C>A		intron_variant				ENSP00000498033

Frequencies

GnomAD3 genomes AF: 0.0725 AC: 11036 AN: 152124 Hom.: 497 Cov.: 31

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.0738

Gnomad SAS AF: 0.0716

Gnomad FIN AF: 0.0536

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0725 AC: 11042 AN: 152242 Hom.: 498 Cov.: 31 AF XY: 0.0715 AC XY: 5321 AN XY: 74428

Gnomad4 AFR AF: 0.0445

Gnomad4 AMR AF: 0.0694

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.0736

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.0536

Gnomad4 NFE AF: 0.0955

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0847 Hom.: 1110

Bravo AF: 0.0725

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.53
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12571363; hg19: chr10-124230612;