rs2645050

Positions:

• chr8-85358432-A-G

Variant summary

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

The NM_001128831.4(CA1):​c.-24-16773T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,196 control chromosomes in the GnomAD database, including 1,353 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 (1353 hom., cov: 33)
• Consequence: CA1 NM_001128831.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA1	NM_001128831.4	c.-24-16773T>C		intron_variant		ENST00000523022.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CA1	ENST00000523022.6	c.-24-16773T>C		intron_variant		1	NM_001128831.4	P1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18198 AN: 152078 Hom.: 1352 Cov.: 33

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0879

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.00634

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.120 AC: 18205 AN: 152196 Hom.: 1353 Cov.: 33 AF XY: 0.119 AC XY: 8881 AN XY: 74382

Gnomad4 AFR AF: 0.0513

Gnomad4 AMR AF: 0.0878

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.00636

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.108

Alfa AF: 0.154 Hom.: 250

Bravo AF: 0.107

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.53

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: rs2645050; hg19: chr8-86270661;