rs7081960

Variant names:

• chr10-68756987-A-G
• rs7081960
• NM_018237.4:c.1837-307A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000265872.11(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 ENST00000265872.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 7 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000265872.11. 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
	CCAR1	NM_018237.4	MANE Select	c.1837-307A>G		intron	N/A	NP_060707.2
	CCAR1	NM_001282959.2		c.1792-307A>G		intron	N/A	NP_001269888.1
	CCAR1	NM_001282960.2		c.1792-307A>G		intron	N/A	NP_001269889.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCAR1	ENST00000265872.11	TSL:1 MANE Select	c.1837-307A>G		intron	N/A	ENSP00000265872.6
	CCAR1	ENST00000543225.5	TSL:1	c.1759-307A>G		intron	N/A	ENSP00000438610.1
	CCAR1	ENST00000536012.5	TSL:1	c.1252-307A>G		intron	N/A	ENSP00000439642.1

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

African (AFR) AF: 0.296 AC: 12254 AN: 41464

American (AMR) AF: 0.177 AC: 2712 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3472

East Asian (EAS) AF: 0.101 AC: 523 AN: 5186

South Asian (SAS) AF: 0.199 AC: 963 AN: 4828

European-Finnish (FIN) AF: 0.159 AC: 1686 AN: 10600

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9245 AN: 67998

Other (OTH) AF: 0.153 AC: 323 AN: 2114

Alfa AF: 0.148 Hom.: 2460

Bravo AF: 0.187

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	22
DANN	Benign	0.80
PhyloP100		1.8
PromoterAI		-0.012	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7081960; hg19: chr10-70516744;