chr16-87897675-A-G

Position:

• chr16-87897675-A-G

Variant summary

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

The NM_001739.2(CA5A):​c.618+4237T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,160 control chromosomes in the GnomAD database, including 9,740 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 0.34 (9740 hom., cov: 33)
• Consequence: CA5A NM_001739.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

CA5A (HGNC:1377): (carbonic anhydrase 5A) 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. CA VA is localized in the mitochondria and expressed primarily in the liver. It may play an important role in ureagenesis and gluconeogenesis. CA5A gene maps to chromosome 16q24.3 and an unprocessed pseudogene has been assigned to 16p12-p11.2. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA5A	NM_001739.2	c.618+4237T>C		intron_variant		ENST00000649794.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CA5A	ENST00000649794.3	c.618+4237T>C		intron_variant			NM_001739.2	P1
CA5A	ENST00000648177.1	c.436+4750T>C		intron_variant
CA5A	ENST00000649158.1	c.618+4237T>C		intron_variant
CA5A	ENST00000648022.1	c.619-3949T>C		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51150 AN: 152042 Hom.: 9705 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.337 AC: 51229 AN: 152160 Hom.: 9740 Cov.: 33 AF XY: 0.333 AC XY: 24751 AN XY: 74396

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.317

Alfa AF: 0.276 Hom.: 8857

Bravo AF: 0.348

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.26
DANN	Benign	0.38

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: rs8058389; hg19: chr16-87931281;