15-63328338-CTTTT-CTTTTTT

Variant names:

• chr15-63328338-C-CTT
• rs57210378
• NM_001218.5:c.875-210_875-209dupAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001218.5(CA12):​c.875-210_875-209dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0055 in 140,396 control chromosomes in the GnomAD database, including 8 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0055 (8 hom., cov: 24)
• Consequence: CA12 NM_001218.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.770

Genes affected

CA12 (HGNC:1371): (carbonic anhydrase 12) 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. This gene product is a type I membrane protein that is highly expressed in normal tissues, such as kidney, colon and pancreas, and has been found to be overexpressed in 10% of clear cell renal carcinomas. Three transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jun 2014]

LOC124903506 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA12	NM_001218.5	c.875-210_875-209dupAA		intron_variant	Intron 8 of 10	ENST00000178638.8	NP_001209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CA12	ENST00000178638.8	c.875-209_875-208insAA		intron_variant	Intron 8 of 10	1	NM_001218.5	ENSP00000178638.3
CA12	ENST00000344366.7	c.875-1106_875-1105insAA		intron_variant	Intron 8 of 9	1		ENSP00000343088.3
CA12	ENST00000422263.2	c.695-1106_695-1105insAA		intron_variant	Intron 7 of 8	2		ENSP00000403028.2
CA12	ENST00000560666.1	n.118-1106_118-1105insAA		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.00551 AC: 773 AN: 140382 Hom.: 9 Cov.: 24

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00348

Gnomad ASJ AF: 0.000596

Gnomad EAS AF: 0.0151

Gnomad SAS AF: 0.00414

Gnomad FIN AF: 0.000983

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000248

Gnomad OTH AF: 0.00476

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

GnomAD4 genome AF: 0.00550 AC: 772 AN: 140396 Hom.: 8 Cov.: 24 AF XY: 0.00570 AC XY: 386 AN XY: 67704

Gnomad4 AFR AF: 0.0157

Gnomad4 AMR AF: 0.00347

Gnomad4 ASJ AF: 0.000596

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.00416

Gnomad4 FIN AF: 0.000983

Gnomad4 NFE AF: 0.000248

Gnomad4 OTH AF: 0.00475

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs57210378; hg19: chr15-63620537;