chr9-120848010-C-T

Position:

• chr9-120848010-C-T

Variant summary

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

The ENST00000640066.2(CUTALP):​n.604+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 ENST00000640066.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

Genes affected

CUTALP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CUTALP	NR_024408.2	n.629+657C>T		intron_variant
CUTALP	NR_152405.1	n.425+657C>T		intron_variant
CUTALP	NR_152406.1	n.2089+657C>T		intron_variant
CUTALP	NR_152407.1	n.182+657C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CUTALP	ENST00000640066.2	n.604+657C>T		intron_variant		1
CUTALP	ENST00000640327.1	n.383+657C>T		intron_variant		1
CUTALP	ENST00000587916.1	n.621+657C>T		intron_variant		3

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

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.534

Alfa AF: 0.575 Hom.: 32830

Bravo AF: 0.476

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837796; hg19: chr9-123610288;