rs17325209

Variant names:

• chr2-48252071-G-A
• rs17325209
• ENST00000650704.1:n.140-8452C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-48252071-G-A
• chr2-48252071-G-C

Variant summary

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

The ENST00000650704.1(ENSG00000230773):​n.140-8452C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0812 in 151,946 control chromosomes in the GnomAD database, including 696 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 0.081 (696 hom., cov: 31)
• Consequence: ENSG00000230773 ENST00000650704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 3 publications found

Genes affected

ENSG00000230773 (HGNC:):

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 = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230773	ENST00000650704.1	n.140-8452C>T		intron_variant	Intron 2 of 5
ENSG00000230773	ENST00000651429.1	n.168+61619C>T		intron_variant	Intron 2 of 8
ENSG00000230773	ENST00000658896.1	n.186+61619C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0813 AC: 12341 AN: 151830 Hom.: 696 Cov.: 31

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0812 AC: 12341 AN: 151946 Hom.: 696 Cov.: 31 AF XY: 0.0794 AC XY: 5893 AN XY: 74254

African (AFR) AF: 0.0280 AC: 1160 AN: 41468

American (AMR) AF: 0.0563 AC: 860 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0398 AC: 138 AN: 3466

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4820

European-Finnish (FIN) AF: 0.144 AC: 1509 AN: 10496

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8373 AN: 67948

Other (OTH) AF: 0.0790 AC: 166 AN: 2102

Alfa AF: 0.0690 Hom.: 122

Bravo AF: 0.0733

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.69
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs17325209; hg19: chr2-48479210;