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. The variant received -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
• Publications: 12 publications found

Genes affected

ENSG00000255496 (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 (NFE) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530663.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255496	ENST00000530663.1	TSL:1	n.148-39553T>C		intron	N/A

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

African (AFR) AF: 0.147 AC: 6110 AN: 41498

American (AMR) AF: 0.350 AC: 5352 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1185 AN: 3464

East Asian (EAS) AF: 0.281 AC: 1447 AN: 5154

South Asian (SAS) AF: 0.361 AC: 1741 AN: 4818

European-Finnish (FIN) AF: 0.552 AC: 5775 AN: 10454

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32949 AN: 67946

Other (OTH) AF: 0.369 AC: 779 AN: 2110

Alfa AF: 0.448 Hom.: 46130

Bravo AF: 0.346

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.71
PhyloP100		0.087

Splicing

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

Other links and lift over

dbSNP: rs1157659; hg19: chr11-27757622;