rs229522

Variant names:

• chr22-37182920-G-A
• rs229522
• NM_031910.4:c.290-185C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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]

ENSG00000235237 (HGNC:40300):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
C1QTNF6	NM_031910.4	c.290-185C>T		intron_variant	Intron 2 of 2	ENST00000337843.7	NP_114116.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF6	ENST00000337843.7	c.290-185C>T		intron_variant	Intron 2 of 2	1	NM_031910.4	ENSP00000338812.2

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

African (AFR) AF: 0.610 AC: 17173 AN: 28154

American (AMR) AF: 0.465 AC: 8744 AN: 18796

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 6634 AN: 18804

East Asian (EAS) AF: 0.469 AC: 16216 AN: 34554

South Asian (SAS) AF: 0.380 AC: 22920 AN: 60270

European-Finnish (FIN) AF: 0.276 AC: 8273 AN: 30022

Middle Eastern (MID) AF: 0.400 AC: 1928 AN: 4824

European-Non Finnish (NFE) AF: 0.256 AC: 262975 AN: 1028828

Other (OTH) AF: 0.333 AC: 17736 AN: 53234

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

African (AFR) AF: 0.592 AC: 24556 AN: 41494

American (AMR) AF: 0.435 AC: 6658 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2541 AN: 5164

South Asian (SAS) AF: 0.376 AC: 1816 AN: 4828

European-Finnish (FIN) AF: 0.260 AC: 2754 AN: 10590

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17980 AN: 67952

Other (OTH) AF: 0.396 AC: 838 AN: 2114

Alfa AF: 0.318 Hom.: 4915

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
PhyloP100		-0.86
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs229522; hg19: chr22-37578960;