15-63327500-GTTTTTT-GTTTTTTTTT

Variant names:

• chr15-63327500-G-GTTT
• rs74794784
• NM_001218.5:c.908-270_908-268dupAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_001218.5(CA12):​c.908-270_908-268dupAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0027 (1 hom., cov: 0)
• Consequence: CA12 NM_001218.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887

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.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00274 (385/140338) while in subpopulation SAS AF= 0.0402 (171/4256). AF 95% confidence interval is 0.0353. There are 1 homozygotes in gnomad4. There are 225 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA12	NM_001218.5	c.908-270_908-268dupAAA		intron_variant	Intron 9 of 10	ENST00000178638.8	NP_001209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CA12	ENST00000178638.8	c.908-268_908-267insAAA		intron_variant	Intron 9 of 10	1	NM_001218.5	ENSP00000178638.3
CA12	ENST00000344366.7	c.875-268_875-267insAAA		intron_variant	Intron 8 of 9	1		ENSP00000343088.3
CA12	ENST00000422263.2	c.695-268_695-267insAAA		intron_variant	Intron 7 of 8	2		ENSP00000403028.2
CA12	ENST00000560666.1	n.118-268_118-267insAAA		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.00275 AC: 386 AN: 140322 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00499

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000637

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00125

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.000117

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000777

Gnomad OTH AF: 0.00213

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

GnomAD4 genome AF: 0.00274 AC: 385 AN: 140338 Hom.: 1 Cov.: 0 AF XY: 0.00332 AC XY: 225 AN XY: 67852

Gnomad4 AFR AF: 0.00499

Gnomad4 AMR AF: 0.000636

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00125

Gnomad4 SAS AF: 0.0402

Gnomad4 FIN AF: 0.000117

Gnomad4 NFE AF: 0.0000777

Gnomad4 OTH AF: 0.00213

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: rs74794784; hg19: chr15-63619699;