rs598988

chr1-78086422-A-G

Variant summary

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

The NM_017655.6(GIPC2):c.426+5562A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,954 control chromosomes in the GnomAD database, including 9,215 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 0.33 (9215 hom., cov: 31)
• Consequence: GIPC2 NM_017655.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

Genes affected

GIPC2 (HGNC:18177): (GIPC PDZ domain containing family member 2) Enables identical protein binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIPC2	NM_017655.6	c.426+5562A>G		intron_variant		ENST00000370759.4
GIPC2	NM_001304725.2	c.204+5562A>G		intron_variant
GIPC2	XM_047423230.1	c.576+5562A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIPC2	ENST00000370759.4	c.426+5562A>G		intron_variant		1	NM_017655.6	P1
GIPC2	ENST00000476882.1	n.264+5562A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50662 AN: 151836 Hom.: 9198 Cov.: 31

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.334 AC: 50709 AN: 151954 Hom.: 9215 Cov.: 31 AF XY: 0.328 AC XY: 24374 AN XY: 74284

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.302

Alfa AF: 0.308 Hom.: 934

Bravo AF: 0.343

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.31

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: rs598988; hg19: chr1-78552106;