rs4922796

Variant names:

• chr11-27811880-C-T
• rs4922796
• ENST00000530663.1:n.147+65622G>A

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.147+65622G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 152,092 control chromosomes in the GnomAD database, including 54,601 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 0.85 (54601 hom., cov: 31)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 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
ENSG00000255496	ENST00000530663.1	n.147+65622G>A		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128496 AN: 151974 Hom.: 54554 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.846 AC: 128594 AN: 152092 Hom.: 54601 Cov.: 31 AF XY: 0.847 AC XY: 62943 AN XY: 74354

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.852

Gnomad4 OTH AF: 0.861

Alfa AF: 0.853 Hom.: 11373

Bravo AF: 0.837

Asia WGS AF: 0.748 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4922796; hg19: chr11-27833427;