rs7829987

Variant names:

• chr8-17604713-T-G
• rs7829987
• NM_001372073.1:c.353+14948T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

ENSG00000287303 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PDGFRL	NM_001372073.1	c.353+14948T>G		intron_variant	Intron 2 of 5	ENST00000251630.11	NP_001359002.1
PDGFRL	NM_006207.2	c.353+14948T>G		intron_variant	Intron 3 of 6		NP_006198.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDGFRL	ENST00000251630.11	c.353+14948T>G		intron_variant	Intron 2 of 5	5	NM_001372073.1	ENSP00000251630.4
ENSG00000287303	ENST00000660331.1	n.1649A>C		non_coding_transcript_exon_variant	Exon 2 of 2
PDGFRL	ENST00000541323.1	c.353+14948T>G		intron_variant	Intron 3 of 6	2		ENSP00000444211.1
PDGFRL	ENST00000673645.1	c.353+14948T>G		intron_variant	Intron 3 of 3			ENSP00000501219.1

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

African (AFR) AF: 0.114 AC: 4743 AN: 41482

American (AMR) AF: 0.121 AC: 1845 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3468

East Asian (EAS) AF: 0.0519 AC: 269 AN: 5184

South Asian (SAS) AF: 0.163 AC: 783 AN: 4816

European-Finnish (FIN) AF: 0.132 AC: 1400 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9284 AN: 67988

Other (OTH) AF: 0.117 AC: 248 AN: 2112

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
PhyloP100		0.077
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7829987; hg19: chr8-17462222;