11-98064519-T-A

Variant names:

• chr11-98064519-T-A
• rs553379
• ENST00000781096.1:n.255-2045A>T

Variant summary

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

The ENST00000781096.1(ENSG00000301727):​n.255-2045A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,084 control chromosomes in the GnomAD database, including 40,969 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 0.73 (40969 hom., cov: 32)
• Consequence: ENSG00000301727 ENST00000781096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 publications found

Genes affected

ENSG00000301727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.809 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
ENSG00000301727	ENST00000781096.1	n.255-2045A>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111305 AN: 151966 Hom.: 40939 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.732 AC: 111386 AN: 152084 Hom.: 40969 Cov.: 32 AF XY: 0.730 AC XY: 54222 AN XY: 74318

African (AFR) AF: 0.678 AC: 28140 AN: 41474

American (AMR) AF: 0.821 AC: 12535 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2663 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3256 AN: 5156

South Asian (SAS) AF: 0.675 AC: 3259 AN: 4826

European-Finnish (FIN) AF: 0.694 AC: 7329 AN: 10566

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51674 AN: 67994

Other (OTH) AF: 0.735 AC: 1556 AN: 2116

Alfa AF: 0.744 Hom.: 5257

Bravo AF: 0.741

Asia WGS AF: 0.673 AC: 2344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.68
DANN	Benign	0.19
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs553379; hg19: chr11-97935247;