rs1157659

Variant names:

• chr11-27736075-A-G
• rs1157659
• ENST00000530663.1:n.148-39553T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-27736075-A-G
• chr11-27736075-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000530663.1(ENSG00000255496):​n.148-39553T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,932 control chromosomes in the GnomAD database, including 12,167 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 0.37 (12167 hom., cov: 31)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

Genes affected

ENSG00000255496 (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 (NFE) allele frequency at 95% confidence interval = 0.481 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
ENSG00000255496	ENST00000530663.1	n.148-39553T>C		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55917 AN: 151814 Hom.: 12162 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.368 AC: 55946 AN: 151932 Hom.: 12167 Cov.: 31 AF XY: 0.367 AC XY: 27265 AN XY: 74242

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.369

Alfa AF: 0.453 Hom.: 32004

Bravo AF: 0.346

Asia WGS AF: 0.331 AC: 1151 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	2.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1157659; hg19: chr11-27757622;