17-48854936-A-G

Variant names:

• chr17-48854936-A-G
• rs8074034
• NM_005831.5:c.913-1156A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_005831.5(CALCOCO2):​c.913-1156A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,958 control chromosomes in the GnomAD database, including 11,284 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 0.34 (11284 hom., cov: 30)
• Consequence: CALCOCO2 NM_005831.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.38
• Publications: 4 publications found

Genes affected

CALCOCO2 (HGNC:29912): (calcium binding and coiled-coil domain 2) This gene encodes a coiled-coil domain-containing protein. The encoded protein functions as a receptor for ubiquitin-coated bacteria and plays an important role in innate immunity by mediating macroautophagy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

ENSG00000293025 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALCOCO2	NM_005831.5	c.913-1156A>G		intron_variant	Intron 9 of 12	ENST00000258947.8	NP_005822.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALCOCO2	ENST00000258947.8	c.913-1156A>G		intron_variant	Intron 9 of 12	1	NM_005831.5	ENSP00000258947.3

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52208 AN: 151840 Hom.: 11289 Cov.: 30

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.343 AC: 52187 AN: 151958 Hom.: 11284 Cov.: 30 AF XY: 0.338 AC XY: 25126 AN XY: 74278

African (AFR) AF: 0.105 AC: 4340 AN: 41488

American (AMR) AF: 0.294 AC: 4482 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3472

East Asian (EAS) AF: 0.101 AC: 524 AN: 5168

South Asian (SAS) AF: 0.306 AC: 1473 AN: 4810

European-Finnish (FIN) AF: 0.479 AC: 5055 AN: 10544

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33538 AN: 67920

Other (OTH) AF: 0.380 AC: 800 AN: 2104

Alfa AF: 0.366 Hom.: 2072

Bravo AF: 0.318

Asia WGS AF: 0.178 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	22
DANN	Benign	0.65
PhyloP100		2.4
Mutation Taster		=99/1	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: rs8074034; hg19: chr17-46932298;