rs10739575

Variant names:

• chr9-120843823-G-A
• rs10739575
• ENST00000640066.3:n.356+384G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-120843823-G-A
• chr9-120843823-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000640066.3(CUTALP):​n.356+384G>A variant causes a intron 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 ENST00000640066.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 18 publications found

Genes affected

CUTALP (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CUTALP	NR_152406.1	n.749G>A		non_coding_transcript_exon_variant	Exon 1 of 4
CUTALP	NR_024408.2	n.365+384G>A		intron_variant	Intron 1 of 3
CUTALP	NR_152405.1	n.365+384G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CUTALP	ENST00000640066.3	n.356+384G>A		intron_variant	Intron 1 of 3	1
CUTALP	ENST00000458394.3	n.749G>A		non_coding_transcript_exon_variant	Exon 1 of 2	2
CUTALP	ENST00000687129.2	n.744G>A		non_coding_transcript_exon_variant	Exon 1 of 1

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

African (AFR) AF: 0.840 AC: 34830 AN: 41448

American (AMR) AF: 0.883 AC: 13462 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3003 AN: 3468

East Asian (EAS) AF: 0.555 AC: 2848 AN: 5132

South Asian (SAS) AF: 0.830 AC: 3983 AN: 4796

European-Finnish (FIN) AF: 0.860 AC: 9063 AN: 10542

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56611 AN: 67942

Other (OTH) AF: 0.840 AC: 1771 AN: 2108

Alfa AF: 0.840 Hom.: 92289

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
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs10739575; hg19: chr9-123606101;