11-64382898-T-C

Variant names:

• chr11-64382898-T-C
• rs559928
• ENST00000757243.1:n.211+9525T>C

Variant summary

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

The ENST00000757243.1(ENSG00000298679):​n.211+9525T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,098 control chromosomes in the GnomAD database, including 46,598 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 0.78 (46598 hom., cov: 31)
• Consequence: ENSG00000298679 ENST00000757243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 60 publications found

Genes affected

ENSG00000298679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.887 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
ENSG00000298679	ENST00000757243.1	n.211+9525T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118100 AN: 151980 Hom.: 46576 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.777 AC: 118171 AN: 152098 Hom.: 46598 Cov.: 31 AF XY: 0.781 AC XY: 58109 AN XY: 74372

African (AFR) AF: 0.632 AC: 26183 AN: 41446

American (AMR) AF: 0.857 AC: 13102 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3112 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4586 AN: 5174

South Asian (SAS) AF: 0.909 AC: 4390 AN: 4828

European-Finnish (FIN) AF: 0.802 AC: 8495 AN: 10586

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55530 AN: 67986

Other (OTH) AF: 0.825 AC: 1743 AN: 2114

Alfa AF: 0.811 Hom.: 216830

Bravo AF: 0.774

Asia WGS AF: 0.883 AC: 3072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.61
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs559928; hg19: chr11-64150370;