11-5231021-T-C

Variant names:

• chr11-5231021-T-C
• rs6578588
• ENST00000759072.1:n.265+5293T>C

Variant summary

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

The ENST00000759072.1(ENSG00000298932):​n.265+5293T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,816 control chromosomes in the GnomAD database, including 26,109 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 0.58 (26109 hom., cov: 30)
• Consequence: ENSG00000298932 ENST00000759072.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 2 publications found

Genes affected

ENSG00000298932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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
ENSG00000298932	ENST00000759072.1	n.265+5293T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87543 AN: 151698 Hom.: 26061 Cov.: 30

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.577 AC: 87654 AN: 151816 Hom.: 26109 Cov.: 30 AF XY: 0.578 AC XY: 42847 AN XY: 74170

African (AFR) AF: 0.692 AC: 28657 AN: 41408

American (AMR) AF: 0.654 AC: 9981 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2278 AN: 3466

East Asian (EAS) AF: 0.780 AC: 4018 AN: 5154

South Asian (SAS) AF: 0.553 AC: 2659 AN: 4808

European-Finnish (FIN) AF: 0.445 AC: 4693 AN: 10540

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33434 AN: 67866

Other (OTH) AF: 0.615 AC: 1298 AN: 2112

Alfa AF: 0.523 Hom.: 3878

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs6578588; hg19: chr11-5252251; COSMIC: COSV53082830;