rs113508841

Variant names:

• chr6-136224135-C-T
• rs113508841
• ENST00000417643.5:n.58+1403G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000417643.5(PDE7B-AS1):​n.58+1403G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 152,158 control chromosomes in the GnomAD database, including 54 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 0.018 (54 hom., cov: 32)
• Consequence: PDE7B-AS1 ENST00000417643.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 1 publications found

Genes affected

PDE7B-AS1 (HGNC:56334): (PDE7B antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.018 (2734/152158) while in subpopulation NFE AF = 0.021 (1431/67998). AF 95% confidence interval is 0.0201. There are 54 homozygotes in GnomAd4. There are 1517 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 54 gene

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
PDE7B-AS1	ENST00000417643.5	n.58+1403G>A		intron_variant	Intron 1 of 7	5
PDE7B-AS1	ENST00000626605.1	n.214+1403G>A		intron_variant	Intron 1 of 5	5
PDE7B-AS1	ENST00000655618.1	n.81+1403G>A		intron_variant	Intron 1 of 7
PDE7B-AS1	ENST00000808454.1	n.131+1403G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0180 AC: 2735 AN: 152040 Hom.: 54 Cov.: 32

Gnomad AFR AF: 0.00365

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.00898

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0144

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

GnomAD4 genome AF: 0.0180 AC: 2734 AN: 152158 Hom.: 54 Cov.: 32 AF XY: 0.0204 AC XY: 1517 AN XY: 74386

African (AFR) AF: 0.00364 AC: 151 AN: 41524

American (AMR) AF: 0.00897 AC: 137 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00519 AC: 18 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.00373 AC: 18 AN: 4820

European-Finnish (FIN) AF: 0.0890 AC: 941 AN: 10568

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0210 AC: 1431 AN: 67998

Other (OTH) AF: 0.0142 AC: 30 AN: 2110

Alfa AF: 0.0192 Hom.: 3

Bravo AF: 0.0117

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.38
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs113508841; hg19: chr6-136545273;