chrX-15676066-A-C

Position:

• chrX-15676066-A-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_026551.2(CA5BP1):​n.130+288A>C variant causes a intron, non coding transcript 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 NR_026551.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

Genes affected

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

CA5BP1-CA5B (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA5BP1	NR_026551.2	n.130+288A>C		intron_variant, non_coding_transcript_variant
CA5BP1-CA5B	NR_160544.1	n.321+288A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CA5BP1	ENST00000380334.6	n.27+494A>C		intron_variant, non_coding_transcript_variant		5
CA5BP1	ENST00000380333.5	n.64+288A>C		intron_variant, non_coding_transcript_variant		2
CA5BP1	ENST00000380336.5	n.37+1098A>C		intron_variant, non_coding_transcript_variant		5
CA5BP1	ENST00000448692.5	n.141+288A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.584 AC: 64447 AN: 110292 Hom.: 13926 Cov.: 22 AF XY: 0.587 AC XY: 19112 AN XY: 32540

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

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.591

Alfa AF: 0.541 Hom.: 4044

Bravo AF: 0.611

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs997294; hg19: chrX-15694189;