rs1782322

Variant names:

• chr10-68726568-T-A
• rs1782322
• NM_018237.4:c.73+3991T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-68726568-T-A
• chr10-68726568-T-G

Variant summary

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

The NM_018237.4(CCAR1):​c.73+3991T>A 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: 30)
• Consequence: CCAR1 NM_018237.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 8 publications found

Genes affected

CCAR1 (HGNC:24236): (cell division cycle and apoptosis regulator 1) Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; nuclear receptor coactivator activity; and transcription corepressor activity. Involved in positive regulation of cell migration and positive regulation of cell population proliferation. Acts upstream of or within positive regulation of apoptotic process. Located in nuclear envelope lumen. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.99).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018237.4. 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
	CCAR1	NM_018237.4	MANE Select	c.73+3991T>A		intron	N/A	NP_060707.2
	CCAR1	NM_001282959.2		c.73+3991T>A		intron	N/A	NP_001269888.1	Q8IX12-2
	CCAR1	NM_001282960.2		c.73+3991T>A		intron	N/A	NP_001269889.1	Q8IX12-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCAR1	ENST00000265872.11	TSL:1 MANE Select	c.73+3991T>A		intron	N/A	ENSP00000265872.6	Q8IX12-1
	CCAR1	ENST00000543225.5	TSL:1	c.73+3991T>A		intron	N/A	ENSP00000438610.1	F5H2E6
	CCAR1	ENST00000536012.5	TSL:1	c.-468+5286T>A		intron	N/A	ENSP00000439642.1	F5H1H2

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.11
PhyloP100		-0.30

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: rs1782322; hg19: chr10-70486325;