rs2553827

Variant names:

• chr11-35075120-G-A
• rs2553827
• ENST00000747995.1:n.136+12281G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-35075120-G-A
• chr11-35075120-G-T

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.136+12281G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,038 control chromosomes in the GnomAD database, including 26,741 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 0.59 (26741 hom., cov: 33)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 4 publications found

Genes affected

ENSG00000297460 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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
ENSG00000297460	ENST00000747995.1	n.136+12281G>A		intron_variant	Intron 2 of 4
ENSG00000297460	ENST00000747996.1	n.85-13318G>A		intron_variant	Intron 1 of 2
ENSG00000297460	ENST00000747997.1	n.84-13318G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89646 AN: 151922 Hom.: 26718 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.590 AC: 89710 AN: 152038 Hom.: 26741 Cov.: 33 AF XY: 0.595 AC XY: 44247 AN XY: 74320

African (AFR) AF: 0.589 AC: 24412 AN: 41460

American (AMR) AF: 0.637 AC: 9733 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2212 AN: 3470

East Asian (EAS) AF: 0.785 AC: 4074 AN: 5188

South Asian (SAS) AF: 0.780 AC: 3757 AN: 4818

European-Finnish (FIN) AF: 0.539 AC: 5687 AN: 10552

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37813 AN: 67964

Other (OTH) AF: 0.620 AC: 1307 AN: 2108

Alfa AF: 0.562 Hom.: 2895

Bravo AF: 0.593

Asia WGS AF: 0.756 AC: 2621 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2553827; hg19: chr11-35096667;