rs9895782

chr17-4705163-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000466297.1(ENSG00000213939):n.55C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0432 in 737,510 control chromosomes in the GnomAD database, including 893 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 0.041 (166 hom., cov: 33)
  • Exomes 𝑓: 0.044 (727 hom.)
• Consequence: ENST00000466297.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.42

Genes affected

(HGNC:):

PELP1-DT (HGNC:55614): (PELP1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PELP1-DT	NR_103482.1	n.142-36G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000466297.1	n.55C>T		non_coding_transcript_exon_variant	1/1
PELP1-DT	ENST00000497885.1	n.142-36G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0411 AC: 6259 AN: 152198 Hom.: 167 Cov.: 33

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0428

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0642

GnomAD4 exome AF: 0.0438 AC: 25607 AN: 585194 Hom.: 727 Cov.: 6 AF XY: 0.0441 AC XY: 13922 AN XY: 315338

Gnomad4 AFR exome AF: 0.0281

Gnomad4 AMR exome AF: 0.0345

Gnomad4 ASJ exome AF: 0.102

Gnomad4 EAS exome AF: 0.000477

Gnomad4 SAS exome AF: 0.0456

Gnomad4 FIN exome AF: 0.0348

Gnomad4 NFE exome AF: 0.0461

Gnomad4 OTH exome AF: 0.0531

GnomAD4 genome AF: 0.0411 AC: 6257 AN: 152316 Hom.: 166 Cov.: 33 AF XY: 0.0418 AC XY: 3115 AN XY: 74486

Gnomad4 AFR AF: 0.0264

Gnomad4 AMR AF: 0.0576

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0424

Gnomad4 FIN AF: 0.0404

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0636

Alfa AF: 0.0513 Hom.: 232

Bravo AF: 0.0428

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	4.0
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9895782; hg19: chr17-4608458;