rs1568889

Variant names:

• chr11-27987916-T-C
• rs1568889
• ENST00000525309.1:n.180-5559A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-27987916-T-C
• chr11-27987916-T-G

Variant summary

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

The ENST00000525309.1(ENSG00000255094):​n.180-5559A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,810 control chromosomes in the GnomAD database, including 3,562 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 0.21 (3562 hom., cov: 32)
• Consequence: ENSG00000255094 ENST00000525309.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691
• Publications: 9 publications found

Genes affected

ENSG00000255094 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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
ENSG00000255094	ENST00000525309.1	n.180-5559A>G		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31911 AN: 151690 Hom.: 3566 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.210 AC: 31892 AN: 151810 Hom.: 3562 Cov.: 32 AF XY: 0.211 AC XY: 15649 AN XY: 74148

African (AFR) AF: 0.154 AC: 6364 AN: 41420

American (AMR) AF: 0.184 AC: 2806 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3468

East Asian (EAS) AF: 0.106 AC: 548 AN: 5152

South Asian (SAS) AF: 0.134 AC: 646 AN: 4812

European-Finnish (FIN) AF: 0.284 AC: 2995 AN: 10536

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17256 AN: 67900

Other (OTH) AF: 0.236 AC: 498 AN: 2106

Alfa AF: 0.236 Hom.: 13591

Bravo AF: 0.201

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.79
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs1568889; hg19: chr11-28009463;