rs10739575

chr9-120843823-G-Achr9-120843823-G-T

Variant summary

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

The NR_152406.1(CUTALP):n.749G>A 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 0.834 in 151,884 control chromosomes in the GnomAD database, including 52,989 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 0.83 (52989 hom., cov: 29)
• Consequence: CUTALP NR_152406.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

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 (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUTALP	NR_152406.1	n.749G>A		non_coding_transcript_exon_variant	1/4
CUTALP	NR_024408.2	n.365+384G>A		intron_variant, non_coding_transcript_variant
CUTALP	NR_152405.1	n.365+384G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUTALP	ENST00000589026.5	n.144-1170G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126512 AN: 151766 Hom.: 52944 Cov.: 29

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.834 AC: 126610 AN: 151884 Hom.: 52989 Cov.: 29 AF XY: 0.835 AC XY: 61969 AN XY: 74226

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.840

Alfa AF: 0.840 Hom.: 73227

Bravo AF: 0.835

Asia WGS AF: 0.716 AC: 2491 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	2.0
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10739575; hg19: chr9-123606101;