rs10489798

Variant names:

• chr1-96779490-A-G
• rs10489798
• NM_021190.4:c.708+1544A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-96779490-A-G
• chr1-96779490-A-T

Variant summary

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

The NM_021190.4(PTBP2):​c.708+1544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 152,144 control chromosomes in the GnomAD database, including 939 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 0.095 (939 hom., cov: 32)
• Consequence: PTBP2 NM_021190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 3 publications found

Genes affected

PTBP2 (HGNC:17662): (polypyrimidine tract binding protein 2) The protein encoded by this gene binds to intronic polypyrimidine clusters in pre-mRNA molecules and is implicated in controlling the assembly of other splicing-regulatory proteins. This protein is very similar to the polypyrimidine tract binding protein (PTB) but most of its isoforms are expressed primarily in the brain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021190.4. 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
	PTBP2	NM_021190.4	MANE Select	c.708+1544A>G		intron	N/A	NP_067013.1
	PTBP2	NM_001300987.2		c.741+1544A>G		intron	N/A	NP_001287916.1
	PTBP2	NM_001300986.2		c.732+1544A>G		intron	N/A	NP_001287915.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTBP2	ENST00000674951.1	MANE Select	c.708+1544A>G		intron	N/A	ENSP00000502818.1
	PTBP2	ENST00000426398.3	TSL:1	c.732+1544A>G		intron	N/A	ENSP00000412788.3
	PTBP2	ENST00000370197.5	TSL:1	c.708+1544A>G		intron	N/A	ENSP00000359216.1

Frequencies

GnomAD3 genomes AF: 0.0949 AC: 14433 AN: 152026 Hom.: 939 Cov.: 32

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.0584

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0949 AC: 14432 AN: 152144 Hom.: 939 Cov.: 32 AF XY: 0.0936 AC XY: 6959 AN XY: 74386

African (AFR) AF: 0.0257 AC: 1068 AN: 41562

American (AMR) AF: 0.0583 AC: 891 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.0548 AC: 264 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1942 AN: 10608

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9583 AN: 67916

Other (OTH) AF: 0.0792 AC: 167 AN: 2108

Alfa AF: 0.0966 Hom.: 562

Bravo AF: 0.0812

Asia WGS AF: 0.0210 AC: 73 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		-0.81
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10489798; hg19: chr1-97245046;