rs113508841

chr6-136224135-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000655618.1(PDE7B-AS1):n.81+1403G>A variant causes a intron, non coding transcript 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 ENST00000655618.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 54 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE7B-AS1	ENST00000655618.1	n.81+1403G>A		intron_variant, non_coding_transcript_variant
PDE7B-AS1	ENST00000417643.5	n.58+1403G>A		intron_variant, non_coding_transcript_variant		5
PDE7B-AS1	ENST00000626605.1	n.214+1403G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.00364

Gnomad4 AMR AF: 0.00897

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00373

Gnomad4 FIN AF: 0.0890

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0142

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113508841; hg19: chr6-136545273;