rs7663443

Positions:

• chr4-15307070-T-C

Variant summary

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

The NR_125911.1(C1QTNF7-AS1):​n.87-43606A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,290 control chromosomes in the GnomAD database, including 873 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 0.067 (873 hom., cov: 33)
• Consequence: C1QTNF7-AS1 NR_125911.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

Genes affected

C1QTNF7-AS1 (HGNC:40683): (C1QTNF7 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF7-AS1	NR_125911.1	n.87-43606A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF7-AS1	ENST00000502344.5	n.87-43606A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0673 AC: 10239 AN: 152172 Hom.: 875 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.00781

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0501

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0673 AC: 10249 AN: 152290 Hom.: 873 Cov.: 33 AF XY: 0.0652 AC XY: 4855 AN XY: 74466

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.0289

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0555

Gnomad4 FIN AF: 0.00781

Gnomad4 NFE AF: 0.0132

Gnomad4 OTH AF: 0.0506

Alfa AF: 0.0445 Hom.: 60

Bravo AF: 0.0739

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7663443; hg19: chr4-15308694;