ENST00000812088.1:n.328-2343T>A

Variant names:

• chr19-48952668-A-T
• rs11667200
• ENST00000812088.1:n.328-2343T>A

Variant summary

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

The ENST00000812088.1(ENSG00000305635):​n.328-2343T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,234 control chromosomes in the GnomAD database, including 60,940 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 0.89 (60940 hom., cov: 32)
• Consequence: ENSG00000305635 ENST00000812088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 10 publications found

Genes affected

ENSG00000305635 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812088.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305635	ENST00000812088.1		n.328-2343T>A		intron	N/A
	ENSG00000305635	ENST00000812089.1		n.472-2343T>A		intron	N/A
	ENSG00000305635	ENST00000812090.1		n.273-2343T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.894 AC: 136020 AN: 152116 Hom.: 60889 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.894 AC: 136130 AN: 152234 Hom.: 60940 Cov.: 32 AF XY: 0.897 AC XY: 66718 AN XY: 74416

African (AFR) AF: 0.913 AC: 37904 AN: 41536

American (AMR) AF: 0.844 AC: 12892 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3173 AN: 3472

East Asian (EAS) AF: 0.952 AC: 4925 AN: 5176

South Asian (SAS) AF: 0.951 AC: 4596 AN: 4832

European-Finnish (FIN) AF: 0.922 AC: 9777 AN: 10602

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 60023 AN: 68026

Other (OTH) AF: 0.877 AC: 1853 AN: 2114

Alfa AF: 0.892 Hom.: 7520

Bravo AF: 0.887

Asia WGS AF: 0.915 AC: 3184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.63
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs11667200; hg19: chr19-49455925;