rs7081960

chr10-68756987-A-G

Variant summary

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

The NM_018237.4(CCAR1):c.1837-307A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,152 control chromosomes in the GnomAD database, including 2,965 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 0.19 (2965 hom., cov: 32)
• Consequence: CCAR1 NM_018237.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCAR1	NM_018237.4	c.1837-307A>G		intron_variant		ENST00000265872.11
CCAR1	NM_001282959.2	c.1792-307A>G		intron_variant
CCAR1	NM_001282960.2	c.1792-307A>G		intron_variant
CCAR1	NR_104262.2	n.1726-307A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCAR1	ENST00000265872.11	c.1837-307A>G		intron_variant		1	NM_018237.4	P1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28091 AN: 152034 Hom.: 2953 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.185 AC: 28149 AN: 152152 Hom.: 2965 Cov.: 32 AF XY: 0.186 AC XY: 13867 AN XY: 74402

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.153

Alfa AF: 0.141 Hom.: 1646

Bravo AF: 0.187

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	22
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		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: rs7081960; hg19: chr10-70516744;