9-120845551-C-T

Position:

• chr9-120845551-C-T

Variant summary

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

The NR_152406.1(CUTALP):​n.2029+355C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 152,298 control chromosomes in the GnomAD database, including 343 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 0.030 (343 hom., cov: 32)
  • Exomes 𝑓: 0.071 (0 hom.)
• Consequence: CUTALP NR_152406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

Genes affected

CUTALP (HGNC:27367): (cutA divalent cation tolerance like, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUTALP	NR_152406.1	n.2029+355C>T		intron_variant, non_coding_transcript_variant
CUTALP	NR_024408.2	n.569+355C>T		intron_variant, non_coding_transcript_variant
CUTALP	NR_152405.1	n.366-1743C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUTALP	ENST00000589026.5	n.347+355C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0295 AC: 4495 AN: 152166 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.00562

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0315

GnomAD4 exome AF: 0.0714 AC: 1 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.0714 AC XY: 1 AN XY: 14

Gnomad4 NFE exome AF: 0.0714

GnomAD4 genome AF: 0.0296 AC: 4500 AN: 152284 Hom.: 343 Cov.: 32 AF XY: 0.0323 AC XY: 2409 AN XY: 74468

Gnomad4 AFR AF: 0.00560

Gnomad4 AMR AF: 0.0135

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.0203

Gnomad4 OTH AF: 0.0345

Alfa AF: 0.0204 Hom.: 74

Bravo AF: 0.0261

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs933003; hg19: chr9-123607829;