11-65745636-T-C

Variant names:

• chr11-65745636-T-C
• rs593982
• ENST00000534505.1:n.-93T>C

Variant summary

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

The ENST00000534505.1(ENSG00000255557):​n.-93T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,196 control chromosomes in the GnomAD database, including 49,341 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 0.80 (49334 hom., cov: 32)
  • Exomes 𝑓: 0.94 (7 hom.)
• Consequence: ENSG00000255557 ENST00000534505.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 20 publications found

Genes affected

ENSG00000255557 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 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
ENSG00000255557	ENST00000534505.1	n.-93T>C		upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121408 AN: 152062 Hom.: 49303 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.805

GnomAD4 exome AF: 0.938 AC: 15 AN: 16 Hom.: 7 AF XY: 1.00 AC XY: 10 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 12 AN: 12

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.798 AC: 121493 AN: 152180 Hom.: 49334 Cov.: 32 AF XY: 0.792 AC XY: 58948 AN XY: 74390

African (AFR) AF: 0.723 AC: 30004 AN: 41510

American (AMR) AF: 0.669 AC: 10221 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2880 AN: 3472

East Asian (EAS) AF: 0.582 AC: 3012 AN: 5174

South Asian (SAS) AF: 0.671 AC: 3232 AN: 4818

European-Finnish (FIN) AF: 0.875 AC: 9266 AN: 10594

Middle Eastern (MID) AF: 0.822 AC: 240 AN: 292

European-Non Finnish (NFE) AF: 0.885 AC: 60198 AN: 68008

Other (OTH) AF: 0.807 AC: 1707 AN: 2116

Alfa AF: 0.851 Hom.: 206416

Bravo AF: 0.778

Asia WGS AF: 0.646 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.28
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs593982; hg19: chr11-65513107;