Genetic Variant CUTALP:n.544+355C>T (chr9-120845551-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000638935.1(CUTALP):n.86C>T variant causes a non coding transcript exon 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
ENST00000638935.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.786

Variant links:

Genes affected

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

CUTALP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	Exon rank
CUTALP	NR_024408.2 link	n.569+355C>T	intron_variant	Intron 2 of 3
CUTALP	NR_152405.1 link	n.366-1743C>T	intron_variant	Intron 1 of 2
CUTALP	NR_152406.1 link	n.2029+355C>T	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CUTALP	ENST00000640066.2 link	n.544+355C>T	intron_variant	Intron 2 of 3	1
CUTALP	ENST00000640327.1 link	n.323+355C>T	intron_variant	Intron 1 of 2	1
CUTALP	ENST00000638935.1 link	n.86C>T	non_coding_transcript_exon_variant	Exon 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.0295

AC:

4495

AN:

152166

Hom.:

342

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.0714

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.0714

GnomAD4 genome

AF:

0.0296

AC:

4500

AN:

152284

Hom.:

343

Cov.:

AF XY:

0.0323

AC XY:

2409

AN XY:

74468

show subpopulations

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.:

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over