17-51653089-A-G

Variant names:

• chr17-51653089-A-G
• rs2106329
• NM_020178.5:c.561+552T>C

Variant summary

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

The NM_020178.5(CA10):​c.561+552T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,054 control chromosomes in the GnomAD database, including 53,101 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 0.83 (53101 hom., cov: 30)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA10	NM_020178.5	c.561+552T>C		intron_variant	Intron 5 of 8	ENST00000451037.7	NP_064563.1
CA10	NM_001082533.1	c.561+552T>C		intron_variant	Intron 6 of 9		NP_001076002.1
CA10	NM_001082534.2	c.561+552T>C		intron_variant	Intron 6 of 9		NP_001076003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CA10	ENST00000451037.7	c.561+552T>C		intron_variant	Intron 5 of 8	1	NM_020178.5	ENSP00000405388.2

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126531 AN: 151936 Hom.: 53065 Cov.: 30

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.833 AC: 126622 AN: 152054 Hom.: 53101 Cov.: 30 AF XY: 0.833 AC XY: 61880 AN XY: 74330

African (AFR) AF: 0.831 AC: 34453 AN: 41464

American (AMR) AF: 0.812 AC: 12403 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3022 AN: 3472

East Asian (EAS) AF: 0.487 AC: 2512 AN: 5158

South Asian (SAS) AF: 0.839 AC: 4033 AN: 4806

European-Finnish (FIN) AF: 0.883 AC: 9336 AN: 10578

Middle Eastern (MID) AF: 0.860 AC: 251 AN: 292

European-Non Finnish (NFE) AF: 0.854 AC: 58076 AN: 67982

Other (OTH) AF: 0.847 AC: 1789 AN: 2112

Alfa AF: 0.844 Hom.: 157530

Bravo AF: 0.826

Asia WGS AF: 0.672 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.6
DANN	Benign	0.21
PhyloP100		0.49
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: rs2106329; hg19: chr17-49730450;