rs17814594

chr8-85342110-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001128831.4(CA1):c.-24-451A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,130 control chromosomes in the GnomAD database, including 1,374 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 0.12 (1374 hom., cov: 32)
• Consequence: CA1 NM_001128831.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

Genes affected

CA1 (HGNC:1368): (carbonic anhydrase 1) Carbonic anhydrases (CAs) are a large family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide. They participate in a variety of biological processes, including respiration, calcification, acid-base balance, bone resorption, and the formation of aqueous humor, cerebrospinal fluid, saliva and gastric acid. They show extensive diversity in tissue distribution and in their subcellular localization. This CA1 gene is closely linked to the CA2 and CA3 genes on chromosome 8. It encodes a cytosolic protein that is found at the highest level in erythrocytes. Allelic variants of this gene have been described in some populations. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Nov 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA1	NM_001128831.4	c.-24-451A>G		intron_variant		ENST00000523022.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CA1	ENST00000523022.6	c.-24-451A>G		intron_variant		1	NM_001128831.4	P1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18629 AN: 152012 Hom.: 1373 Cov.: 32

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00731

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.123 AC: 18641 AN: 152130 Hom.: 1374 Cov.: 32 AF XY: 0.122 AC XY: 9055 AN XY: 74352

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.0848

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00733

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.116

Alfa AF: 0.156 Hom.: 2530

Bravo AF: 0.110

Asia WGS AF: 0.0920 AC: 314 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.6
Dann	Benign	0.86

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

Publications

LitVar

Other links and lift over

dbSNP: rs17814594; hg19: chr8-86254339;