11-69234875-T-C

Variant names:

• chr11-69234875-T-C
• rs11228580
• ENST00000779509.1:n.139-13486T>C

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.139-13486T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,074 control chromosomes in the GnomAD database, including 1,817 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 0.15 (1817 hom., cov: 31)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 18 publications found

Genes affected

ENSG00000301530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369367	NR_188530.1	n.54+6A>G		splice_region_variant, intron_variant	Intron 1 of 3
LOC105369367	NR_188531.1	n.54+6A>G		splice_region_variant, intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301530	ENST00000779509.1	n.139-13486T>C		intron_variant	Intron 1 of 3
ENSG00000301550	ENST00000779653.1	n.30+6A>G		splice_region_variant, intron_variant	Intron 1 of 4
ENSG00000301550	ENST00000779654.1	n.55+6A>G		splice_region_variant, intron_variant	Intron 1 of 3
ENSG00000301530	ENST00000779510.1	n.-186T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22690 AN: 151954 Hom.: 1817 Cov.: 31

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.00697

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0838

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.149 AC: 22702 AN: 152074 Hom.: 1817 Cov.: 31 AF XY: 0.145 AC XY: 10765 AN XY: 74336

African (AFR) AF: 0.165 AC: 6851 AN: 41464

American (AMR) AF: 0.120 AC: 1831 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3472

East Asian (EAS) AF: 0.00679 AC: 35 AN: 5156

South Asian (SAS) AF: 0.0760 AC: 366 AN: 4816

European-Finnish (FIN) AF: 0.0838 AC: 886 AN: 10574

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11394 AN: 67978

Other (OTH) AF: 0.176 AC: 371 AN: 2108

Alfa AF: 0.160 Hom.: 1066

Bravo AF: 0.155

Asia WGS AF: 0.0590 AC: 203 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.30
DANN	Benign	0.49
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11228580; hg19: chr11-69002342;