rs1150345

Variant names:

• chr11-95641373-A-C
• rs1150345
• ENST00000648353.1:n.525+69165A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-95641373-A-C
• chr11-95641373-A-T

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.525+69165A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,068 control chromosomes in the GnomAD database, including 37,605 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 0.70 (37605 hom., cov: 32)
• Consequence: ENSG00000285842 ENST00000648353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 1 publications found

Genes affected

ENSG00000285842 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 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
ENSG00000285842	ENST00000648353.1	n.525+69165A>C		intron_variant	Intron 3 of 4
ENSG00000306211	ENST00000816277.1	n.498-26209T>G		intron_variant	Intron 1 of 4
ENSG00000306211	ENST00000816278.1	n.113-26209T>G		intron_variant	Intron 1 of 2
ENSG00000306211	ENST00000816279.1	n.81-26209T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106355 AN: 151950 Hom.: 37558 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.700 AC: 106456 AN: 152068 Hom.: 37605 Cov.: 32 AF XY: 0.702 AC XY: 52166 AN XY: 74346

African (AFR) AF: 0.748 AC: 31014 AN: 41482

American (AMR) AF: 0.623 AC: 9516 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2025 AN: 3466

East Asian (EAS) AF: 0.660 AC: 3411 AN: 5172

South Asian (SAS) AF: 0.783 AC: 3765 AN: 4810

European-Finnish (FIN) AF: 0.719 AC: 7605 AN: 10578

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46905 AN: 67960

Other (OTH) AF: 0.698 AC: 1478 AN: 2116

Alfa AF: 0.690 Hom.: 106773

Bravo AF: 0.689

Asia WGS AF: 0.737 AC: 2559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.85
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1150345; hg19: chr11-95374537;