4-15334809-A-G

Position:

• chr4-15334809-A-G

Variant summary

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

The NR_125911.1(C1QTNF7-AS1):​n.87-71345T>C 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 0.569 in 152,048 control chromosomes in the GnomAD database, including 25,249 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 0.57 (25249 hom., cov: 32)
• Consequence: C1QTNF7-AS1 NR_125911.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

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=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF7-AS1	NR_125911.1	n.87-71345T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF7-AS1	ENST00000502344.5	n.87-71345T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86508 AN: 151930 Hom.: 25222 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.569 AC: 86587 AN: 152048 Hom.: 25249 Cov.: 32 AF XY: 0.572 AC XY: 42518 AN XY: 74298

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.534

Alfa AF: 0.456 Hom.: 1853

Bravo AF: 0.560

Asia WGS AF: 0.607 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6449126; hg19: chr4-15336433;