5-35210220-C-T

Position:

• chr5-35210220-C-T

Variant summary

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

The NM_000949.7(PRLR):​c.-106+20048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,094 control chromosomes in the GnomAD database, including 2,767 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 0.15 (2767 hom., cov: 32)
• Consequence: PRLR NM_000949.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

PRLR (HGNC:9446): (prolactin receptor) This gene encodes a receptor for the anterior pituitary hormone, prolactin, and belongs to the type I cytokine receptor family. Prolactin-dependent signaling occurs as the result of ligand-induced dimerization of the prolactin receptor. Several alternatively spliced transcript variants encoding different membrane-bound and soluble isoforms have been described for this gene, which may function to modulate the endocrine and autocrine effects of prolactin in normal tissue and cancer. [provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRLR	NM_000949.7	c.-106+20048G>A		intron_variant		ENST00000618457.5	NP_000940.1
PRLR	XM_024446131.2	c.59+20048G>A		intron_variant			XP_024301899.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRLR	ENST00000618457.5	c.-106+20048G>A		intron_variant		1	NM_000949.7	ENSP00000482954	P1
PRLR	ENST00000504500.5	c.-293+20048G>A		intron_variant		3		ENSP00000422867
PRLR	ENST00000515839.1	c.-268-14507G>A		intron_variant		2		ENSP00000421864
PRLR	ENST00000508107.5	c.-106+20048G>A		intron_variant, NMD_transcript_variant		3		ENSP00000427236

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23279 AN: 151976 Hom.: 2760 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.153 AC: 23320 AN: 152094 Hom.: 2767 Cov.: 32 AF XY: 0.150 AC XY: 11162 AN XY: 74356

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.0894

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.152

Alfa AF: 0.126 Hom.: 209

Bravo AF: 0.159

Asia WGS AF: 0.0680 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.67

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: rs34024951; hg19: chr5-35210322;