chr4-15241045-T-G

Position:

• chr4-15241045-T-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.154+22352A>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 0.213 in 152,136 control chromosomes in the GnomAD database, including 4,157 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 0.21 (4157 hom., cov: 32)
• Consequence: C1QTNF7-AS1 NR_125911.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF7-AS1	NR_125911.1	n.154+22352A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF7-AS1	ENST00000502344.5	n.154+22352A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32433 AN: 152018 Hom.: 4157 Cov.: 32

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.213 AC: 32426 AN: 152136 Hom.: 4157 Cov.: 32 AF XY: 0.218 AC XY: 16232 AN XY: 74362

Gnomad4 AFR AF: 0.0908

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.210

Alfa AF: 0.192 Hom.: 756

Bravo AF: 0.188

Asia WGS AF: 0.227 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.61
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35933199; hg19: chr4-15242669;