rs11232369

Variant names:

• chr11-80851695-G-A
• rs11232369
• ENST00000795280.1:n.80-3886C>T

Variant summary

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

The ENST00000795280.1(ENSG00000303527):​n.80-3886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0571 in 152,022 control chromosomes in the GnomAD database, including 425 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 0.057 (425 hom., cov: 32)
• Consequence: ENSG00000303527 ENST00000795280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 1 publications found

Genes affected

ENSG00000303527 (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 (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795280.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303527	ENST00000795280.1		n.80-3886C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8653 AN: 151904 Hom.: 423 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.0204

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0571 AC: 8673 AN: 152022 Hom.: 425 Cov.: 32 AF XY: 0.0566 AC XY: 4205 AN XY: 74300

African (AFR) AF: 0.118 AC: 4897 AN: 41446

American (AMR) AF: 0.0420 AC: 641 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3468

East Asian (EAS) AF: 0.0486 AC: 251 AN: 5164

South Asian (SAS) AF: 0.0204 AC: 98 AN: 4810

European-Finnish (FIN) AF: 0.0463 AC: 489 AN: 10562

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0299 AC: 2032 AN: 67990

Other (OTH) AF: 0.0634 AC: 133 AN: 2098

Alfa AF: 0.0391 Hom.: 601

Bravo AF: 0.0601

Asia WGS AF: 0.0400 AC: 140 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.63
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs11232369; hg19: chr11-80562738;