rs2276120

Variant names:

• chr11-67497208-C-A
• rs2276120
• NM_004910.3:c.2146+23G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-67497208-C-A
• chr11-67497208-C-G
• chr11-67497208-C-T

Variant summary

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

The NM_004910.3(PITPNM1):​c.2146+23G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000712 in 1,404,850 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 7.1e-7 (0 hom.)
• Consequence: PITPNM1 NM_004910.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 0 publications found

Genes affected

PITPNM1 (HGNC:9003): (phosphatidylinositol transfer protein membrane associated 1) PITPNM1 belongs to a family of membrane-associated phosphatidylinositol transfer domain-containing proteins that share homology with the Drosophila retinal degeneration B (rdgB) protein (Ocaka et al., 2005 [PubMed 15627748]).[supplied by OMIM, Mar 2008]

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=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITPNM1	NM_004910.3	c.2146+23G>T		intron_variant	Intron 14 of 23	ENST00000356404.8	NP_004901.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITPNM1	ENST00000356404.8	c.2146+23G>T		intron_variant	Intron 14 of 23	1	NM_004910.3	ENSP00000348772.3
PITPNM1	ENST00000534749.5	c.2146+23G>T		intron_variant	Intron 13 of 22	1		ENSP00000437286.1
PITPNM1	ENST00000436757.7	c.2146+23G>T		intron_variant	Intron 14 of 23	1		ENSP00000398787.2
PITPNM1	ENST00000527370.5	n.1000G>T		non_coding_transcript_exon_variant	Exon 4 of 13	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.12e-7 AC: 1 AN: 1404850 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 693018

African (AFR) AF: 0.00 AC: 0 AN: 31572

American (AMR) AF: 0.00 AC: 0 AN: 37694

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23526

East Asian (EAS) AF: 0.00 AC: 0 AN: 38540

South Asian (SAS) AF: 0.00 AC: 0 AN: 80532

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50782

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4468

European-Non Finnish (NFE) AF: 9.26e-7 AC: 1 AN: 1080036

Other (OTH) AF: 0.00 AC: 0 AN: 57700

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.85
PhyloP100		-0.14
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs2276120; hg19: chr11-67264679;