chr17-67002887-T-G

Variant names:

• chr17-67002887-T-G
• rs8071936
• NM_014405.4:c.221-15302T>G

Variant summary

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

The NM_014405.4(CACNG4):​c.221-15302T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,134 control chromosomes in the GnomAD database, including 4,411 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 0.16 (4411 hom., cov: 32)
• Consequence: CACNG4 NM_014405.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 4 publications found

Genes affected

CACNG4 (HGNC:1408): (calcium voltage-gated channel auxiliary subunit gamma 4) The protein encoded by this gene is a type I transmembrane AMPA receptor regulatory protein (TARP). TARPs regulate both trafficking and channel gating of the AMPA receptors. This gene is part of a functionally diverse eight-member protein subfamily of the PMP-22/EMP/MP20 family and is located in a cluster with two family members, a type II TARP and a calcium channel gamma subunit. [provided by RefSeq, Dec 2010]

ENSG00000300392 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014405.4. 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
	CACNG4	NM_014405.4	MANE Select	c.221-15302T>G		intron	N/A	NP_055220.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNG4	ENST00000262138.4	TSL:1 MANE Select	c.221-15302T>G		intron	N/A	ENSP00000262138.3
	ENSG00000300392	ENST00000771276.1		n.310+2632A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23709 AN: 152016 Hom.: 4393 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0240

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.156 AC: 23775 AN: 152134 Hom.: 4411 Cov.: 32 AF XY: 0.154 AC XY: 11430 AN XY: 74396

African (AFR) AF: 0.442 AC: 18308 AN: 41462

American (AMR) AF: 0.114 AC: 1746 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1191 AN: 5156

South Asian (SAS) AF: 0.0879 AC: 424 AN: 4826

European-Finnish (FIN) AF: 0.0107 AC: 114 AN: 10612

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0240 AC: 1635 AN: 68008

Other (OTH) AF: 0.113 AC: 238 AN: 2110

Alfa AF: 0.0658 Hom.: 5304

Bravo AF: 0.178

Asia WGS AF: 0.152 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.87
DANN	Benign	0.49
PhyloP100		-0.31
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: rs8071936; hg19: chr17-64999003;