9-17514517-A-G

Position:

• chr9-17514517-A-G

Variant summary

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

The XR_007061321.1(CNTLN):​n.4346+4496A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,088 control chromosomes in the GnomAD database, including 35,075 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 0.62 (35075 hom., cov: 32)
• Consequence: CNTLN XR_007061321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

CNTLN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTLN	XR_007061321.1	n.4346+4496A>G		intron_variant, non_coding_transcript_variant
CNTLN	XR_007061322.1	n.4343+4496A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94510 AN: 151970 Hom.: 35075 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.621 AC: 94515 AN: 152088 Hom.: 35075 Cov.: 32 AF XY: 0.628 AC XY: 46701 AN XY: 74332

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.658

Alfa AF: 0.746 Hom.: 19817

Bravo AF: 0.602

Asia WGS AF: 0.816 AC: 2835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1885167; hg19: chr9-17514515; COSMIC: COSV60336233;