rs7296859

Variant names:

• chr12-6784998-C-G
• rs7296859
• ENST00000747991.1:n.282G>C

Variant summary

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

The ENST00000747991.1(ENSG00000297457):​n.282G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,092 control chromosomes in the GnomAD database, including 41,282 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 0.73 (41282 hom., cov: 32)
• Consequence: ENSG00000297457 ENST00000747991.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 13 publications found

Genes affected

ENSG00000297457 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297457	ENST00000747991.1	n.282G>C		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110900 AN: 151974 Hom.: 41231 Cov.: 32

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.730 AC: 111007 AN: 152092 Hom.: 41282 Cov.: 32 AF XY: 0.728 AC XY: 54099 AN XY: 74336

African (AFR) AF: 0.874 AC: 36255 AN: 41500

American (AMR) AF: 0.653 AC: 9968 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2226 AN: 3468

East Asian (EAS) AF: 0.715 AC: 3699 AN: 5172

South Asian (SAS) AF: 0.642 AC: 3091 AN: 4814

European-Finnish (FIN) AF: 0.758 AC: 8012 AN: 10568

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45355 AN: 67992

Other (OTH) AF: 0.701 AC: 1481 AN: 2112

Alfa AF: 0.702 Hom.: 4693

Bravo AF: 0.732

Asia WGS AF: 0.680 AC: 2370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7296859; hg19: chr12-6894164;