ENST00000774790.1:n.249-19166G>T

Variant names:

• chr11-93599319-C-A
• rs11020442
• ENST00000774790.1:n.249-19166G>T

Variant summary

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

The ENST00000774790.1(ENSG00000300871):​n.249-19166G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,130 control chromosomes in the GnomAD database, including 4,066 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 0.19 (4066 hom., cov: 33)
• Consequence: ENSG00000300871 ENST00000774790.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 0 publications found

Genes affected

ENSG00000300871 (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 = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774790.1. 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
	ENSG00000300871	ENST00000774790.1		n.249-19166G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28935 AN: 152012 Hom.: 4055 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0724

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.190 AC: 28980 AN: 152130 Hom.: 4066 Cov.: 33 AF XY: 0.185 AC XY: 13787 AN XY: 74380

African (AFR) AF: 0.401 AC: 16632 AN: 41460

American (AMR) AF: 0.120 AC: 1829 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3470

East Asian (EAS) AF: 0.154 AC: 799 AN: 5172

South Asian (SAS) AF: 0.105 AC: 506 AN: 4822

European-Finnish (FIN) AF: 0.0724 AC: 767 AN: 10598

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7505 AN: 67998

Other (OTH) AF: 0.185 AC: 391 AN: 2112

Alfa AF: 0.132 Hom.: 2913

Bravo AF: 0.207

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.31
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11020442; hg19: chr11-93332485;