NM_006277.3:c.1345-83G>C

Variant names:

• chr2-24298897-C-G
• rs6707600
• NM_006277.3:c.1345-83G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006277.3(ITSN2):​c.1345-83G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ITSN2 NM_006277.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 12 publications found

Genes affected

ITSN2 (HGNC:6184): (intersectin 2) This gene encodes a cytoplasmic protein which contains SH3 domains. This protein is a member of a family of proteins involved in clathrin-mediated endocytosis. Intersectin 2 is thought to regulate the formation of clathrin-coated vesicles and also may function in the induction of T cell antigen receptor (TCR) endocytosis. [provided by RefSeq, Jan 2017]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006277.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITSN2	NM_006277.3	MANE Select	c.1345-83G>C		intron	N/A	NP_006268.2
	ITSN2	NM_001348181.2		c.1303-83G>C		intron	N/A	NP_001335110.1
	ITSN2	NM_019595.4		c.1345-83G>C		intron	N/A	NP_062541.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITSN2	ENST00000355123.9	TSL:1 MANE Select	c.1345-83G>C		intron	N/A	ENSP00000347244.4
	ITSN2	ENST00000361999.7	TSL:1	c.1345-83G>C		intron	N/A	ENSP00000354561.2
	ITSN2	ENST00000406921.7	TSL:1	c.1345-83G>C		intron	N/A	ENSP00000384499.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1186870 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 595908

African (AFR) AF: 0.00 AC: 0 AN: 26424

American (AMR) AF: 0.00 AC: 0 AN: 29374

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19848

East Asian (EAS) AF: 0.00 AC: 0 AN: 37810

South Asian (SAS) AF: 0.00 AC: 0 AN: 66376

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41076

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4632

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 910818

Other (OTH) AF: 0.00 AC: 0 AN: 50512

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.061

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: rs6707600; hg19: chr2-24521766;