12-3705072-G-A

Variant names:

• chr12-3705072-G-A
• rs10848911
• NM_001144958.2:c.-36-8037C>T

Variant summary

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

The NM_001144958.2(CRACR2A):​c.-36-8037C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,170 control chromosomes in the GnomAD database, including 3,338 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 (3338 hom., cov: 33)
• Consequence: CRACR2A NM_001144958.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.910
• Publications: 10 publications found

Genes affected

CRACR2A (HGNC:28657): (calcium release activated channel regulator 2A) Enables GTPase activity and calcium ion binding activity. Involved in several processes, including activation of store-operated calcium channel activity; positive regulation of JNK cascade; and store-operated calcium entry. Located in several cellular components, including Golgi apparatus; Weibel-Palade body; and immunological synapse. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144958.2. 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
	CRACR2A	NM_001144958.2	MANE Select	c.-36-8037C>T		intron	N/A	NP_001138430.1
	CRACR2A	NM_032680.4		c.-36-8037C>T		intron	N/A	NP_116069.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRACR2A	ENST00000440314.7	TSL:2 MANE Select	c.-36-8037C>T		intron	N/A	ENSP00000409382.2
	CRACR2A	ENST00000252322.1	TSL:1	c.-36-8037C>T		intron	N/A	ENSP00000252322.1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28988 AN: 152052 Hom.: 3337 Cov.: 33

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.191 AC: 28993 AN: 152170 Hom.: 3338 Cov.: 33 AF XY: 0.196 AC XY: 14591 AN XY: 74390

African (AFR) AF: 0.0540 AC: 2242 AN: 41546

American (AMR) AF: 0.248 AC: 3786 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1303 AN: 5182

South Asian (SAS) AF: 0.218 AC: 1050 AN: 4820

European-Finnish (FIN) AF: 0.321 AC: 3388 AN: 10560

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15715 AN: 67988

Other (OTH) AF: 0.205 AC: 434 AN: 2114

Alfa AF: 0.212 Hom.: 8298

Bravo AF: 0.181

Asia WGS AF: 0.217 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.44
PhyloP100		0.91
Mutation Taster		=100/0	polymorphism (auto)

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: rs10848911; hg19: chr12-3814238;