4-15241045-T-G

Variant names:

• chr4-15241045-T-G
• rs35933199
• ENST00000502344.6:n.154+22352A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000502344.6(C1QTNF7-AS1):​n.154+22352A>C variant causes a intron 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 ENST00000502344.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502344.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7-AS1	NR_125911.1		n.154+22352A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7-AS1	ENST00000502344.6	TSL:3	n.154+22352A>C		intron	N/A

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

African (AFR) AF: 0.0908 AC: 3771 AN: 41536

American (AMR) AF: 0.152 AC: 2329 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1019 AN: 3472

East Asian (EAS) AF: 0.175 AC: 905 AN: 5178

South Asian (SAS) AF: 0.298 AC: 1433 AN: 4814

European-Finnish (FIN) AF: 0.370 AC: 3912 AN: 10564

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18147 AN: 67980

Other (OTH) AF: 0.210 AC: 444 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.61
DANN	Benign	0.75
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs35933199; hg19: chr4-15242669;