rs7829987

chr8-17604713-T-G

Variant summary

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

The NM_001372073.1(PDGFRL):c.353+14948T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,122 control chromosomes in the GnomAD database, including 1,211 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 0.13 (1211 hom., cov: 32)
• Consequence: PDGFRL NM_001372073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

PDGFRL (HGNC:8805): (platelet derived growth factor receptor like) This gene encodes a protein with significant sequence similarity to the ligand binding domain of platelet-derived growth factor receptor beta. Mutations in this gene, or deletion of a chromosomal segment containing this gene, are associated with sporadic hepatocellular carcinomas, colorectal cancers, and non-small cell lung cancers. This suggests this gene product may function as a tumor suppressor. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDGFRL	NM_001372073.1	c.353+14948T>G		intron_variant		ENST00000251630.11
PDGFRL	NM_006207.2	c.353+14948T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDGFRL	ENST00000251630.11	c.353+14948T>G		intron_variant		5	NM_001372073.1	P1
	ENST00000660331.1	n.1649A>C		non_coding_transcript_exon_variant	2/2
PDGFRL	ENST00000541323.1	c.353+14948T>G		intron_variant		2		P1
PDGFRL	ENST00000673645.1	c.353+14948T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19284 AN: 152004 Hom.: 1207 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.127 AC: 19305 AN: 152122 Hom.: 1211 Cov.: 32 AF XY: 0.127 AC XY: 9454 AN XY: 74376

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0519

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.117

Alfa AF: 0.125 Hom.: 144

Bravo AF: 0.126

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	5.7
Dann	Benign	0.93

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

Publications

LitVar

Other links and lift over

dbSNP: rs7829987; hg19: chr8-17462222;