Genetic Variant ENSG00000235237:n.209-2397C>T (chr22-37180032-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000419128.1(ENSG00000235237):n.209-2397C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,240 control chromosomes in the GnomAD database, including 11,173 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 0.36 ( 11171 hom., cov: 34)

Exomes 𝑓: 0.35 ( 2 hom. )

Consequence

ENSG00000235237
ENST00000419128.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.509

Variant links:

Genes affected

ENSG00000235237 (HGNC:40300):

ENSG00000235237 links:

C1QTNF6 (HGNC:14343): (C1q and TNF related 6) Predicted to enable identical protein binding activity. Predicted to be located in extracellular space. Predicted to be integral component of membrane. Predicted to be part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

C1QTNF6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF6	NM_031910.4 link	c.*2156G>A		downstream_gene_variant		ENST00000337843.7	NP_114116.3	Q9BXI9-2A0A024R1J0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF6	ENST00000337843.7 link	c.*2156G>A		downstream_gene_variant		1	NM_031910.4	ENSP00000338812.2		Q9BXI9-2

Frequencies

GnomAD3 genomes

AF:

0.364

AC:

55318

AN:

152074

Hom.:

11134

Cov.:

show subpopulations

Gnomad AFR

AF:

0.516

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.428

Gnomad ASJ

AF:

0.372

Gnomad EAS

AF:

0.491

Gnomad SAS

AF:

0.365

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.383

GnomAD4 exome

AF:

0.354

AC:

AN:

Hom.:

AF XY:

0.361

AC XY:

AN XY:

show subpopulations

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.292

Gnomad4 NFE exome

AF:

0.300

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.364

AC:

55428

AN:

152192

Hom.:

11171

Cov.:

AF XY:

0.367

AC XY:

27285

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.516

Gnomad4 AMR

AF:

0.428

Gnomad4 ASJ

AF:

0.372

Gnomad4 EAS

AF:

0.492

Gnomad4 SAS

AF:

0.367

Gnomad4 FIN

AF:

0.260

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.384

Alfa

AF:

0.326

Hom.:

2697

Bravo

AF:

0.387

Asia WGS

AF:

0.457

AC:

1588

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.0

DANN

Benign

0.69

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over