rs7350278

chr9-17524040-G-T

Variant summary

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

The XR_007061321.1(CNTLN):n.4347-4348G>T 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 0.187 in 152,160 control chromosomes in the GnomAD database, including 3,455 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 0.19 (3455 hom., cov: 33)
• Consequence: CNTLN XR_007061321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

Genes affected

CNTLN (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 (NFE) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTLN	XR_007061321.1	n.4347-4348G>T		intron_variant, non_coding_transcript_variant
CNTLN	XR_007061322.1	n.4344-4348G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28415 AN: 152042 Hom.: 3458 Cov.: 33

Gnomad AFR AF: 0.0563

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.187 AC: 28410 AN: 152160 Hom.: 3455 Cov.: 33 AF XY: 0.183 AC XY: 13628 AN XY: 74392

Gnomad4 AFR AF: 0.0561

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.224

Alfa AF: 0.260 Hom.: 10589

Bravo AF: 0.176

Asia WGS AF: 0.0920 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.6
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7350278; hg19: chr9-17524038;