chr7-24283306-CTG-C

Variant names:

• chr7-24283306-CTG-C
• rs3037354
• ENST00000746097.1:n.626_627delCA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000746097.1(ENSG00000297196):​n.626_627delCA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6174 hom., cov: 19)
• Consequence: ENSG00000297196 ENST00000746097.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 14 publications found

Genes affected

ENSG00000297196 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746097.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297196	ENST00000746097.1		n.626_627delCA		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000297196	ENST00000746098.1		n.681_682delCA		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000228944	ENST00000718234.1		n.319+36049_319+36050delCA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42663 AN: 151926 Hom.: 6166 Cov.: 19

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.281 AC: 42692 AN: 152044 Hom.: 6174 Cov.: 19 AF XY: 0.280 AC XY: 20794 AN XY: 74336

African (AFR) AF: 0.343 AC: 14230 AN: 41460

American (AMR) AF: 0.223 AC: 3407 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1598 AN: 5178

South Asian (SAS) AF: 0.298 AC: 1433 AN: 4812

European-Finnish (FIN) AF: 0.251 AC: 2653 AN: 10562

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17463 AN: 67954

Other (OTH) AF: 0.285 AC: 601 AN: 2110

Alfa AF: 0.268 Hom.: 710

Bravo AF: 0.281

Asia WGS AF: 0.310 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs3037354; hg19: chr7-24322925;