chr11-56672760-C-T

Position:

• chr11-56672760-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641232.1(ENSG00000290752):​n.180-1340G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 143,990 control chromosomes in the GnomAD database, including 28,749 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 0.60 (28749 hom., cov: 30)
• Consequence: ENST00000641232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641232.1	n.180-1340G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.604 AC: 86929 AN: 143864 Hom.: 28734 Cov.: 30

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.604 AC: 86964 AN: 143990 Hom.: 28749 Cov.: 30 AF XY: 0.609 AC XY: 42761 AN XY: 70242

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.643

Alfa AF: 0.650 Hom.: 38023

Asia WGS AF: 0.725 AC: 2513 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11228719; hg19: chr11-56440236;