rs598988

Variant names:

• chr1-78086422-A-G
• rs598988
• NM_017655.6:c.426+5562A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017655.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIPC2	NM_017655.6	MANE Select	c.426+5562A>G		intron	N/A	NP_060125.4
	GIPC2	NM_001304725.2		c.204+5562A>G		intron	N/A	NP_001291654.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIPC2	ENST00000370759.4	TSL:1 MANE Select	c.426+5562A>G		intron	N/A	ENSP00000359795.3	Q8TF65
	GIPC2	ENST00000911079.1		c.576+5562A>G		intron	N/A	ENSP00000581138.1
	GIPC2	ENST00000911082.1		c.426+5562A>G		intron	N/A	ENSP00000581141.1

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

African (AFR) AF: 0.475 AC: 19684 AN: 41436

American (AMR) AF: 0.231 AC: 3531 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1071 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2544 AN: 5166

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4820

European-Finnish (FIN) AF: 0.244 AC: 2582 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19238 AN: 67918

Other (OTH) AF: 0.302 AC: 638 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.31
PhyloP100		-0.88
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: rs598988; hg19: chr1-78552106;