11-69152181-A-G

Variant names:

• chr11-69152181-A-G
• rs2290419
• ENST00000562772.1:n.478-4441T>C

Variant summary

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

The ENST00000562772.1(ENSG00000261070):​n.478-4441T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 151,768 control chromosomes in the GnomAD database, including 258 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 0.048 (258 hom., cov: 31)
• Consequence: ENSG00000261070 ENST00000562772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.739
• Publications: 9 publications found

Genes affected

ENSG00000261070 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC338694	NR_104161.1	n.476-4441T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261070	ENST00000562772.1	n.478-4441T>C		intron_variant	Intron 2 of 2	1
ENSG00000287725	ENST00000637084.1	n.*512-7265A>G		intron_variant	Intron 14 of 14	1		ENSP00000490615.1
ENSG00000287725	ENST00000692585.1	n.*512-7265A>G		intron_variant	Intron 14 of 14			ENSP00000509200.1
ENSG00000261070	ENST00000822204.1	n.220+726T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0484 AC: 7334 AN: 151650 Hom.: 258 Cov.: 31

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0549

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0209

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.0671

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

GnomAD4 genome AF: 0.0483 AC: 7329 AN: 151768 Hom.: 258 Cov.: 31 AF XY: 0.0487 AC XY: 3604 AN XY: 74078

African (AFR) AF: 0.0137 AC: 569 AN: 41422

American (AMR) AF: 0.0548 AC: 834 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3470

East Asian (EAS) AF: 0.0799 AC: 412 AN: 5156

South Asian (SAS) AF: 0.142 AC: 677 AN: 4770

European-Finnish (FIN) AF: 0.0209 AC: 219 AN: 10454

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0580 AC: 3939 AN: 67962

Other (OTH) AF: 0.0659 AC: 139 AN: 2108

Alfa AF: 0.0570 Hom.: 130

Bravo AF: 0.0473

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.4
DANN	Benign	0.67
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs2290419; hg19: chr11-68919649;