ENST00000822754.1:n.233-7913G>A

Variant names:

• chr11-127486377-G-A
• rs1729076
• ENST00000822754.1:n.233-7913G>A

Variant summary

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

The ENST00000822754.1(ENSG00000307024):​n.233-7913G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,856 control chromosomes in the GnomAD database, including 15,298 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 0.44 (15298 hom., cov: 31)
• Consequence: ENSG00000307024 ENST00000822754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 3 publications found

Genes affected

ENSG00000307024 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822754.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307024	ENST00000822754.1		n.233-7913G>A		intron	N/A
	ENSG00000307024	ENST00000822755.1		n.270-9785G>A		intron	N/A
	ENSG00000307024	ENST00000822756.1		n.224-9785G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67312 AN: 151738 Hom.: 15294 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.444 AC: 67359 AN: 151856 Hom.: 15298 Cov.: 31 AF XY: 0.444 AC XY: 32951 AN XY: 74212

African (AFR) AF: 0.546 AC: 22624 AN: 41402

American (AMR) AF: 0.418 AC: 6388 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1625 AN: 3472

East Asian (EAS) AF: 0.292 AC: 1503 AN: 5148

South Asian (SAS) AF: 0.486 AC: 2331 AN: 4794

European-Finnish (FIN) AF: 0.424 AC: 4463 AN: 10534

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27046 AN: 67926

Other (OTH) AF: 0.408 AC: 857 AN: 2102

Alfa AF: 0.419 Hom.: 28744

Bravo AF: 0.446

Asia WGS AF: 0.418 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.48
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1729076; hg19: chr11-127356272;