rs13393791

chr2-3256295-T-C

Variant summary

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

The NM_003310.5(EIPR1):c.416+1004A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,110 control chromosomes in the GnomAD database, including 908 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 0.11 (908 hom., cov: 33)
• Consequence: EIPR1 NM_003310.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590

Genes affected

EIPR1 (HGNC:12383): (EARP complex and GARP complex interacting protein 1) This gene has been reported in PMID 9403053 as one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. Alignment of this gene to genomic sequence data suggests that this gene resides on chromosome 2 rather than chromosome 11. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EIPR1	NM_003310.5	c.416+1004A>G		intron_variant		ENST00000382125.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EIPR1	ENST00000382125.9	c.416+1004A>G		intron_variant		1	NM_003310.5	P1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16265 AN: 151992 Hom.: 908 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0733

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0971

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.107 AC: 16288 AN: 152110 Hom.: 908 Cov.: 33 AF XY: 0.108 AC XY: 8049 AN XY: 74342

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.0676

Gnomad4 ASJ AF: 0.0733

Gnomad4 EAS AF: 0.0581

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.0971

Gnomad4 OTH AF: 0.0854

Alfa AF: 0.0962 Hom.: 681

Bravo AF: 0.0998

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.0
Dann	Benign	0.48

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: rs13393791; hg19: chr2-3260066;