rs3213239

Positions:

• chr19-43576907-G-GGGCC
• chr19-43576907-G-GGGCCGGCC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001193621.3(PINLYP):​c.-88_-85dupGCCG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.63 (30159 hom., cov: 0)
  • Exomes 𝑓: 0.62 (55683 hom.)
• Consequence: PINLYP NM_001193621.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

PINLYP (HGNC:44206): (phospholipase A2 inhibitor and LY6/PLAUR domain containing) Predicted to enable phospholipase inhibitor activity. Predicted to be involved in negative regulation of catalytic activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000268361 (HGNC:):

XRCC1 (HGNC:12828): (X-ray repair cross complementing 1) The protein encoded by this gene is involved in the efficient repair of DNA single-strand breaks formed by exposure to ionizing radiation and alkylating agents. This protein interacts with DNA ligase III, polymerase beta and poly (ADP-ribose) polymerase to participate in the base excision repair pathway. It may play a role in DNA processing during meiogenesis and recombination in germ cells. A rare microsatellite polymorphism in this gene is associated with cancer in patients of varying radiosensitivity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PINLYP	NM_001193621.3	c.-88_-85dupGCCG		5_prime_UTR_variant	1/6	ENST00000599207.6	NP_001180550.2
PINLYP	XM_047438830.1	c.-211_-208dupGCCG		5_prime_UTR_variant	1/5		XP_047294786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PINLYP	ENST00000599207	c.-88_-85dupGCCG		5_prime_UTR_variant	1/6	5	NM_001193621.3	ENSP00000469886.1
ENSG00000268361	ENST00000594374.1	c.169-15891_169-15888dupGGCC		intron_variant		3		ENSP00000472698.1

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95042 AN: 151248 Hom.: 30144 Cov.: 0

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.705

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.641

GnomAD4 exome AF: 0.616 AC: 172214 AN: 279460 Hom.: 55683 Cov.: 4 AF XY: 0.613 AC XY: 89371 AN XY: 145734

Gnomad4 AFR exome AF: 0.616

Gnomad4 AMR exome AF: 0.755

Gnomad4 ASJ exome AF: 0.665

Gnomad4 EAS exome AF: 0.889

Gnomad4 SAS exome AF: 0.598

Gnomad4 FIN exome AF: 0.543

Gnomad4 NFE exome AF: 0.580

Gnomad4 OTH exome AF: 0.620

GnomAD4 genome AF: 0.628 AC: 95104 AN: 151366 Hom.: 30159 Cov.: 0 AF XY: 0.630 AC XY: 46602 AN XY: 73940

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.642

Alfa AF: 0.477 Hom.: 1258

Bravo AF: 0.647

Asia WGS AF: 0.744 AC: 2583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3213239; hg19: chr19-44081059;