rs2728127

Variant names:

• chr4-87973963-A-G
• rs2728127
• ENST00000829025.1:n.-240T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-87973963-A-G
• chr4-87973963-A-T

Variant summary

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

The ENST00000829025.1(ENSG00000307815):​n.-240T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,140 control chromosomes in the GnomAD database, including 11,252 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 0.37 (11252 hom., cov: 33)
• Consequence: ENSG00000307815 ENST00000829025.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 19 publications found

Genes affected

ENSG00000307815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900730	XR_007058172.1	n.-194T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307815	ENST00000829025.1	n.-240T>C		upstream_gene_variant
ENSG00000307815	ENST00000829040.1	n.-220T>C		upstream_gene_variant
ENSG00000307815	ENST00000829041.1	n.-229T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55933 AN: 152022 Hom.: 11228 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.368 AC: 56002 AN: 152140 Hom.: 11252 Cov.: 33 AF XY: 0.368 AC XY: 27382 AN XY: 74402

African (AFR) AF: 0.535 AC: 22197 AN: 41486

American (AMR) AF: 0.282 AC: 4307 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3468

East Asian (EAS) AF: 0.364 AC: 1887 AN: 5180

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4824

European-Finnish (FIN) AF: 0.365 AC: 3860 AN: 10584

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20293 AN: 67984

Other (OTH) AF: 0.355 AC: 751 AN: 2114

Alfa AF: 0.327 Hom.: 5275

Bravo AF: 0.368

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.3
DANN	Benign	0.62
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2728127; hg19: chr4-88895115;