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. Variant got -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

Genes affected

ENSG00000285842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.698

Alfa AF: 0.682 Hom.: 44462

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1150345; hg19: chr11-95374537;