chr12-70488947-T-C

Variant names:

• chr12-70488947-T-C
• rs1603225
• ENST00000548687.5:n.243+20620T>C

Variant summary

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

The ENST00000548687.5(PTPRB-AS1):​n.243+20620T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 146,690 control chromosomes in the GnomAD database, including 2,103 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 0.16 (2103 hom., cov: 32)
• Consequence: PTPRB-AS1 ENST00000548687.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 1 publications found

Genes affected

PTPRB-AS1 (HGNC:58150):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548687.5. 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
	PTPRB-AS1	ENST00000548687.5	TSL:1	n.243+20620T>C		intron	N/A
	PTPRB-AS1	ENST00000548924.5	TSL:3	n.219-18948T>C		intron	N/A
	PTPRB-AS1	ENST00000549359.5	TSL:4	n.206-18948T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 22907 AN: 146574 Hom.: 2103 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00126

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.156 AC: 22904 AN: 146690 Hom.: 2103 Cov.: 32 AF XY: 0.153 AC XY: 10886 AN XY: 71298

African (AFR) AF: 0.0736 AC: 2869 AN: 38998

American (AMR) AF: 0.143 AC: 2079 AN: 14518

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 450 AN: 3440

East Asian (EAS) AF: 0.00126 AC: 6 AN: 4748

South Asian (SAS) AF: 0.0876 AC: 387 AN: 4420

European-Finnish (FIN) AF: 0.181 AC: 1833 AN: 10114

Middle Eastern (MID) AF: 0.0931 AC: 27 AN: 290

European-Non Finnish (NFE) AF: 0.220 AC: 14797 AN: 67220

Other (OTH) AF: 0.145 AC: 296 AN: 2038

Alfa AF: 0.187 Hom.: 2363

Bravo AF: 0.145

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.55
PhyloP100		0.13

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: rs1603225;

hg19: chr12-70882727;