chr22-37185231-G-A

Position:

• chr22-37185231-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Moderate BP6_Moderate BS2

The NM_031910.4(C1QTNF6):​c.276C>T​(p.Ile92=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00325 in 1,566,592 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0026 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0033 (9 hom.)
• Consequence: C1QTNF6 NM_031910.4 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.769

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BP6: Variant 22-37185231-G-A is Benign according to our data. Variant chr22-37185231-G-A is described in ClinVar as [Benign]. Clinvar id is 774971.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF6	NM_031910.4	c.276C>T	p.Ile92=	synonymous_variant	2/3	ENST00000337843.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF6	ENST00000337843.7	c.276C>T	p.Ile92=	synonymous_variant	2/3	1	NM_031910.4	P1

Frequencies

GnomAD3 genomes AF: 0.00263 AC: 400 AN: 152188 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000844

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.00510

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00362

Gnomad OTH AF: 0.00335

GnomAD3 exomes AF: 0.00245 AC: 529 AN: 215674 Hom.: 1 AF XY: 0.00255 AC XY: 294 AN XY: 115212

Gnomad AFR exome AF: 0.000450

Gnomad AMR exome AF: 0.00311

Gnomad ASJ exome AF: 0.00847

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000472

Gnomad FIN exome AF: 0.000154

Gnomad NFE exome AF: 0.00341

Gnomad OTH exome AF: 0.00432

GnomAD4 exome AF: 0.00332 AC: 4691 AN: 1414286 Hom.: 9 Cov.: 30 AF XY: 0.00323 AC XY: 2254 AN XY: 697896

Gnomad4 AFR exome AF: 0.000340

Gnomad4 AMR exome AF: 0.00316

Gnomad4 ASJ exome AF: 0.00781

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000430

Gnomad4 FIN exome AF: 0.000193

Gnomad4 NFE exome AF: 0.00379

Gnomad4 OTH exome AF: 0.00352

GnomAD4 genome AF: 0.00263 AC: 400 AN: 152306 Hom.: 1 Cov.: 32 AF XY: 0.00242 AC XY: 180 AN XY: 74468

Gnomad4 AFR AF: 0.000842

Gnomad4 AMR AF: 0.00510

Gnomad4 ASJ AF: 0.00806

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00362

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00334 Hom.: 1

Bravo AF: 0.00286

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 13, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	5.7
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs77643619; hg19: chr22-37581271;