rs997294

Variant names:

• chrX-15676066-A-C
• rs997294
• ENST00000380333.5:n.64+288A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000380333.5(CA5BP1):​n.64+288A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.58 (13944 hom., 19168 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: CA5BP1 ENST00000380333.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 1 publications found

Genes affected

CA5BP1 (HGNC:):

CA5BP1 (HGNC:29544): (carbonic anhydrase 5B pseudogene 1)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000380333.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CA5BP1	NR_026551.2		n.130+288A>C		intron	N/A
	CA5BP1	NR_160541.1		n.41+1110A>C		intron	N/A
	CA5BP1	NR_160542.1		n.115+494A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CA5BP1	ENST00000380333.5	TSL:2	n.64+288A>C		intron	N/A
	CA5BP1	ENST00000380334.6	TSL:5	n.27+494A>C		intron	N/A
	CA5BP1	ENST00000380336.5	TSL:5	n.37+1098A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.584 AC: 64447 AN: 110292 Hom.: 13926 Cov.: 22

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.585

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.585 AC: 64526 AN: 110345 Hom.: 13944 Cov.: 22 AF XY: 0.588 AC XY: 19168 AN XY: 32603

African (AFR) AF: 0.710 AC: 21497 AN: 30286

American (AMR) AF: 0.679 AC: 7096 AN: 10454

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1312 AN: 2635

East Asian (EAS) AF: 0.939 AC: 3286 AN: 3500

South Asian (SAS) AF: 0.668 AC: 1753 AN: 2624

European-Finnish (FIN) AF: 0.512 AC: 2975 AN: 5813

Middle Eastern (MID) AF: 0.486 AC: 103 AN: 212

European-Non Finnish (NFE) AF: 0.480 AC: 25244 AN: 52643

Other (OTH) AF: 0.591 AC: 894 AN: 1513

Alfa AF: 0.541 Hom.: 4044

Bravo AF: 0.611

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.61
PhyloP100		-0.018

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs997294;

hg19: chrX-15694189;