17-51779485-C-A

Variant names:

• chr17-51779485-C-A
• rs1526189
• NM_020178.5:c.280-31667G>T

Variant summary

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

The NM_020178.5(CA10):​c.280-31667G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,024 control chromosomes in the GnomAD database, including 24,003 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 0.52 (24003 hom., cov: 31)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 4 publications found

Genes affected

CA10 (HGNC:1369): (carbonic anhydrase 10) This gene encodes a protein that belongs to the carbonic anhydrase family of zinc metalloenzymes, which catalyze the reversible hydration of carbon dioxide in various biological processes. The protein encoded by this gene is an acatalytic member of the alpha-carbonic anhydrase subgroup, and it is thought to play a role in the central nervous system, especially in brain development. Multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

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 (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020178.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CA10	NM_020178.5	MANE Select	c.280-31667G>T		intron	N/A	NP_064563.1
	CA10	NM_001082533.1		c.280-31667G>T		intron	N/A	NP_001076002.1
	CA10	NM_001082534.2		c.280-31667G>T		intron	N/A	NP_001076003.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CA10	ENST00000451037.7	TSL:1 MANE Select	c.280-31667G>T		intron	N/A	ENSP00000405388.2
	CA10	ENST00000285273.8	TSL:1	c.280-31667G>T		intron	N/A	ENSP00000285273.4
	CA10	ENST00000442502.6	TSL:1	c.280-31667G>T		intron	N/A	ENSP00000390666.2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78718 AN: 151906 Hom.: 24004 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.518 AC: 78744 AN: 152024 Hom.: 24003 Cov.: 31 AF XY: 0.530 AC XY: 39356 AN XY: 74300

African (AFR) AF: 0.170 AC: 7053 AN: 41484

American (AMR) AF: 0.673 AC: 10276 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2186 AN: 3466

East Asian (EAS) AF: 0.687 AC: 3546 AN: 5158

South Asian (SAS) AF: 0.608 AC: 2922 AN: 4804

European-Finnish (FIN) AF: 0.742 AC: 7835 AN: 10564

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42899 AN: 67968

Other (OTH) AF: 0.556 AC: 1172 AN: 2108

Alfa AF: 0.594 Hom.: 88302

Bravo AF: 0.500

Asia WGS AF: 0.626 AC: 2174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	17
DANN	Benign	0.73
PhyloP100		1.0
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: rs1526189; hg19: chr17-49856845;