rs2014307

Variant names:

• chr10-122458116-T-G
• rs2014307
• ENST00000647969.1:n.182+379A>C

Variant summary

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

The ENST00000647969.1(HTRA1-AS1):​n.182+379A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,900 control chromosomes in the GnomAD database, including 30,025 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 0.63 (30025 hom., cov: 31)
• Consequence: HTRA1-AS1 ENST00000647969.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 19 publications found

Genes affected

HTRA1-AS1 (HGNC:58122):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647969.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTRA1-AS1	ENST00000647969.1		n.182+379A>C		intron	N/A
	HTRA1-AS1	ENST00000650300.1		n.1852+379A>C		intron	N/A
	HTRA1-AS1	ENST00000811415.1		n.373+379A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.626 AC: 94974 AN: 151782 Hom.: 29977 Cov.: 31

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.626 AC: 95075 AN: 151900 Hom.: 30025 Cov.: 31 AF XY: 0.621 AC XY: 46092 AN XY: 74226

African (AFR) AF: 0.716 AC: 29647 AN: 41424

American (AMR) AF: 0.557 AC: 8509 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1928 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3450 AN: 5132

South Asian (SAS) AF: 0.621 AC: 2980 AN: 4802

European-Finnish (FIN) AF: 0.532 AC: 5608 AN: 10540

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40864 AN: 67952

Other (OTH) AF: 0.622 AC: 1313 AN: 2110

Alfa AF: 0.615 Hom.: 94743

Bravo AF: 0.629

Asia WGS AF: 0.672 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	8.4
DANN	Benign	0.76
PhyloP100		0.062
PromoterAI		0.079	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2014307;

hg19: chr10-124217632;