22-37190752-C-T

Variant names:

• chr22-37190752-C-T
• rs2160908
• NM_001365878.1:c.-7+113G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
C1QTNF6	NM_001365878.1	c.-7+113G>A		intron_variant	Intron 3 of 4		NP_001352807.1
C1QTNF6	XM_024452150.2	c.-126+113G>A		intron_variant	Intron 3 of 5		XP_024307918.1
C1QTNF6	XM_024452153.2	c.-126+113G>A		intron_variant	Intron 3 of 5		XP_024307921.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF6	ENST00000467564.5	n.355-75G>A		intron_variant	Intron 4 of 4	3
C1QTNF6	ENST00000470655.5	n.3051+113G>A		intron_variant	Intron 3 of 8	2
C1QTNF6	ENST00000497071.1	n.564-75G>A		intron_variant	Intron 5 of 5	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.410 AC: 16906 AN: 41258

American (AMR) AF: 0.494 AC: 7528 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3466

East Asian (EAS) AF: 0.725 AC: 3758 AN: 5180

South Asian (SAS) AF: 0.478 AC: 2302 AN: 4812

European-Finnish (FIN) AF: 0.307 AC: 3142 AN: 10234

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.308 AC: 20931 AN: 67862

Other (OTH) AF: 0.407 AC: 855 AN: 2100

Alfa AF: 0.345 Hom.: 1199

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2160908; hg19: chr22-37586792;