rs1150345

Positions:

• 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, non coding transcript 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: ENST00000648353.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648353.1	n.525+69165A>C		intron_variant, non_coding_transcript_variant

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;