ENST00000591646.1:n.114-476T>C

Variant names:

• chr19-44951502-A-G
• rs7247227
• ENST00000591646.1:n.114-476T>C

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.114-476T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,576 control chromosomes in the GnomAD database, including 20,042 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 0.51 (20042 hom., cov: 30)
• Consequence: ENSG00000267114 ENST00000591646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 8 publications found

Genes affected

ENSG00000267114 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 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
ENSG00000267114	ENST00000591646.1	n.114-476T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77057 AN: 151456 Hom.: 20009 Cov.: 30

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.509 AC: 77138 AN: 151576 Hom.: 20042 Cov.: 30 AF XY: 0.511 AC XY: 37874 AN XY: 74066

African (AFR) AF: 0.578 AC: 23876 AN: 41308

American (AMR) AF: 0.566 AC: 8604 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1542 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2823 AN: 5118

South Asian (SAS) AF: 0.580 AC: 2794 AN: 4816

European-Finnish (FIN) AF: 0.487 AC: 5125 AN: 10530

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30839 AN: 67824

Other (OTH) AF: 0.491 AC: 1033 AN: 2106

Alfa AF: 0.485 Hom.: 3593

Bravo AF: 0.519

Asia WGS AF: 0.577 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.092
DANN	Benign	0.48
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7247227; hg19: chr19-45454759; COSMIC: COSV52991016;