rs2462907

Variant names:

• chr7-27087612-T-C
• rs2462907
• ENST00000748170.1:n.767A>G

Variant summary

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

The ENST00000748170.1(ENSG00000297475):​n.767A>G 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 0.487 in 151,866 control chromosomes in the GnomAD database, including 18,218 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 0.49 (18218 hom., cov: 31)
• Consequence: ENSG00000297475 ENST00000748170.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 8 publications found

Genes affected

ENSG00000297475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 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
ENSG00000297475	ENST00000748170.1	n.767A>G		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000297475	ENST00000748166.1	n.262+237A>G		intron_variant	Intron 1 of 2
ENSG00000297475	ENST00000748167.1	n.206+237A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73972 AN: 151748 Hom.: 18205 Cov.: 31

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.487 AC: 74033 AN: 151866 Hom.: 18218 Cov.: 31 AF XY: 0.482 AC XY: 35750 AN XY: 74186

African (AFR) AF: 0.522 AC: 21586 AN: 41390

American (AMR) AF: 0.446 AC: 6817 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1903 AN: 3466

East Asian (EAS) AF: 0.411 AC: 2116 AN: 5144

South Asian (SAS) AF: 0.437 AC: 2098 AN: 4802

European-Finnish (FIN) AF: 0.399 AC: 4204 AN: 10536

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33519 AN: 67946

Other (OTH) AF: 0.494 AC: 1041 AN: 2106

Alfa AF: 0.492 Hom.: 11802

Bravo AF: 0.492

Asia WGS AF: 0.431 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.24
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2462907; hg19: chr7-27127231;