rs229522

Positions:

• chr22-37182920-G-A

Variant summary

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

The NM_031910.4(C1QTNF6):​c.290-185C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 1,429,598 control chromosomes in the GnomAD database, including 68,274 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 0.39 (12982 hom., cov: 33)
  • Exomes 𝑓: 0.28 (55292 hom.)
• Consequence: C1QTNF6 NM_031910.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1QTNF6	NM_031910.4	c.290-185C>T		intron_variant		ENST00000337843.7	NP_114116.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1QTNF6	ENST00000337843.7	c.290-185C>T		intron_variant		1	NM_031910.4	ENSP00000338812	P1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58636 AN: 151994 Hom.: 12920 Cov.: 33

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.396

GnomAD4 exome AF: 0.284 AC: 362599 AN: 1277486 Hom.: 55292 Cov.: 32 AF XY: 0.286 AC XY: 176573 AN XY: 618420

Gnomad4 AFR exome AF: 0.610

Gnomad4 AMR exome AF: 0.465

Gnomad4 ASJ exome AF: 0.353

Gnomad4 EAS exome AF: 0.469

Gnomad4 SAS exome AF: 0.380

Gnomad4 FIN exome AF: 0.276

Gnomad4 NFE exome AF: 0.256

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.386 AC: 58775 AN: 152112 Hom.: 12982 Cov.: 33 AF XY: 0.388 AC XY: 28856 AN XY: 74348

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.396

Alfa AF: 0.320 Hom.: 4475

Bravo AF: 0.412

Asia WGS AF: 0.469 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs229522; hg19: chr22-37578960;