chr22-37190752-C-T

Position:

• chr22-37190752-C-T

Variant summary

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

The NM_001365878.1(C1QTNF6):​c.-7+113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,362 control chromosomes in the GnomAD database, including 11,497 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 0.38 (11497 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: C1QTNF6 NM_001365878.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF6	NM_001365878.1	c.-7+113G>A		intron_variant
C1QTNF6	XM_011529857.3	c.-7+113G>A		intron_variant
C1QTNF6	XM_024452150.2	c.-126+113G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF6	ENST00000467564.5	n.355-75G>A		intron_variant, non_coding_transcript_variant		3
C1QTNF6	ENST00000470655.5	n.3051+113G>A		intron_variant, non_coding_transcript_variant		2
C1QTNF6	ENST00000497071.1	n.564-75G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57147 AN: 151266 Hom.: 11466 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.400

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.378 AC: 57219 AN: 151362 Hom.: 11497 Cov.: 32 AF XY: 0.384 AC XY: 28355 AN XY: 73894

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.407

Alfa AF: 0.343 Hom.: 1145

Bravo AF: 0.396

Asia WGS AF: 0.616 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	12
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2160908; hg19: chr22-37586792;