rs7250467

Variant names:

• chr19-28078494-T-G
• rs7250467
• ENST00000586671.5:n.99+13129T>G

Variant summary

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

The ENST00000586671.5(ENSG00000267509):​n.99+13129T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,934 control chromosomes in the GnomAD database, including 10,594 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 (10594 hom., cov: 31)
• Consequence: ENSG00000267509 ENST00000586671.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 1 publications found

Genes affected

ENSG00000267509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 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
ENSG00000267509	ENST00000586671.5	n.99+13129T>G		intron_variant	Intron 1 of 3	4
ENSG00000267509	ENST00000590229.2	n.99+13129T>G		intron_variant	Intron 1 of 4	4
ENSG00000267509	ENST00000722298.1	n.99+13129T>G		intron_variant	Intron 1 of 1
ENSG00000267509	ENST00000722299.1	n.193+7119T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55535 AN: 151814 Hom.: 10593 Cov.: 31

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.366 AC: 55549 AN: 151934 Hom.: 10594 Cov.: 31 AF XY: 0.362 AC XY: 26864 AN XY: 74256

African (AFR) AF: 0.284 AC: 11782 AN: 41432

American (AMR) AF: 0.380 AC: 5808 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3464

East Asian (EAS) AF: 0.239 AC: 1232 AN: 5148

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4814

European-Finnish (FIN) AF: 0.379 AC: 3997 AN: 10556

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28790 AN: 67928

Other (OTH) AF: 0.374 AC: 791 AN: 2114

Alfa AF: 0.402 Hom.: 53446

Bravo AF: 0.366

Asia WGS AF: 0.205 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.48
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7250467; hg19: chr19-28569401;