11-80855353-C-A

Variant names:

• chr11-80855353-C-A
• rs1355652
• ENST00000795280.1:n.80-7544G>T

Variant summary

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

The ENST00000795280.1(ENSG00000303527):​n.80-7544G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,914 control chromosomes in the GnomAD database, including 11,516 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 0.38 (11516 hom., cov: 32)
• Consequence: ENSG00000303527 ENST00000795280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303527	ENST00000795280.1		n.80-7544G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57264 AN: 151796 Hom.: 11521 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.377 AC: 57278 AN: 151914 Hom.: 11516 Cov.: 32 AF XY: 0.383 AC XY: 28424 AN XY: 74252

African (AFR) AF: 0.286 AC: 11868 AN: 41440

American (AMR) AF: 0.430 AC: 6547 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3716 AN: 5164

South Asian (SAS) AF: 0.501 AC: 2411 AN: 4816

European-Finnish (FIN) AF: 0.387 AC: 4073 AN: 10532

Middle Eastern (MID) AF: 0.417 AC: 121 AN: 290

European-Non Finnish (NFE) AF: 0.378 AC: 25658 AN: 67950

Other (OTH) AF: 0.423 AC: 893 AN: 2110

Alfa AF: 0.386 Hom.: 21844

Bravo AF: 0.377

Asia WGS AF: 0.552 AC: 1920 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	6.5
DANN	Benign	0.55
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1355652; hg19: chr11-80566396;