rs229541

Positions:

• chr22-37195278-G-A
• chr22-37195278-G-C
• chr22-37195278-G-T

Variant summary

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

The NM_001365878.1(C1QTNF6):​c.-71+2325C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,102 control chromosomes in the GnomAD database, including 19,317 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 0.49 (19316 hom., cov: 33)
  • Exomes 𝑓: 0.63 (1 hom.)
• Consequence: C1QTNF6 NM_001365878.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF6	NM_001365878.1	c.-71+2325C>T		intron_variant
C1QTNF6	XM_011529857.3	c.-71+103C>T		intron_variant
C1QTNF6	XM_024452150.2	c.-190+103C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF6	ENST00000467564.5	n.224+103C>T		intron_variant, non_coding_transcript_variant		3
C1QTNF6	ENST00000470655.5	n.2921+103C>T		intron_variant, non_coding_transcript_variant		2
C1QTNF6	ENST00000497071.1	n.433+103C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75077 AN: 151976 Hom.: 19288 Cov.: 33

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.497

GnomAD4 exome AF: 0.625 AC: 5 AN: 8 Hom.: 1 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.494 AC: 75147 AN: 152094 Hom.: 19316 Cov.: 33 AF XY: 0.493 AC XY: 36636 AN XY: 74366

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.495

Alfa AF: 0.446 Hom.: 21434

Bravo AF: 0.511

Asia WGS AF: 0.558 AC: 1938 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	0.44
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: rs229541; hg19: chr22-37591318;