9-120848010-C-T

Variant names:

• chr9-120848010-C-T
• rs4837796
• ENST00000640066.3:n.620+657C>T

Variant summary

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

The ENST00000640066.3(CUTALP):​n.620+657C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,990 control chromosomes in the GnomAD database, including 20,333 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 0.49 (20333 hom., cov: 32)
• Consequence: CUTALP ENST00000640066.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 52 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640066.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CUTALP	NR_024408.2		n.629+657C>T		intron	N/A
	CUTALP	NR_152405.1		n.425+657C>T		intron	N/A
	CUTALP	NR_152406.1		n.2089+657C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CUTALP	ENST00000640066.3	TSL:1	n.620+657C>T		intron	N/A
	CUTALP	ENST00000640327.1	TSL:1	n.383+657C>T		intron	N/A
	CUTALP	ENST00000587916.2	TSL:3	n.771+657C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74103 AN: 151872 Hom.: 20320 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.488 AC: 74134 AN: 151990 Hom.: 20333 Cov.: 32 AF XY: 0.496 AC XY: 36881 AN XY: 74284

African (AFR) AF: 0.220 AC: 9130 AN: 41452

American (AMR) AF: 0.626 AC: 9549 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2255 AN: 3470

East Asian (EAS) AF: 0.474 AC: 2451 AN: 5170

South Asian (SAS) AF: 0.735 AC: 3547 AN: 4824

European-Finnish (FIN) AF: 0.587 AC: 6188 AN: 10550

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39356 AN: 67948

Other (OTH) AF: 0.534 AC: 1126 AN: 2108

Alfa AF: 0.565 Hom.: 40615

Bravo AF: 0.476

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		-0.80

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4837796;

hg19: chr9-123610288;