rs7153027

Variant names:

• chr14-91960878-A-C
• rs7153027
• ENST00000828662.1:n.194+2497T>G

Variant summary

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

The ENST00000828662.1(ENSG00000307754):​n.194+2497T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,656 control chromosomes in the GnomAD database, including 15,049 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 0.44 (15049 hom., cov: 30)
• Consequence: ENSG00000307754 ENST00000828662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 43 publications found

Genes affected

ENSG00000307754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000828662.1. 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
	ENSG00000307754	ENST00000828662.1		n.194+2497T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66272 AN: 151538 Hom.: 15041 Cov.: 30

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.437 AC: 66298 AN: 151656 Hom.: 15049 Cov.: 30 AF XY: 0.431 AC XY: 31930 AN XY: 74090

African (AFR) AF: 0.545 AC: 22504 AN: 41310

American (AMR) AF: 0.296 AC: 4507 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3468

East Asian (EAS) AF: 0.275 AC: 1417 AN: 5158

South Asian (SAS) AF: 0.387 AC: 1866 AN: 4816

European-Finnish (FIN) AF: 0.411 AC: 4309 AN: 10472

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28601 AN: 67878

Other (OTH) AF: 0.422 AC: 889 AN: 2106

Alfa AF: 0.426 Hom.: 68417

Bravo AF: 0.434

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	1.8
DANN	Benign	0.95
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7153027; hg19: chr14-92427222;