ENST00000530177.2:n.707+3829G>A

Variant names:

• chr11-127057517-G-A
• rs674237
• ENST00000530177.2:n.707+3829G>A

Variant summary

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

The ENST00000530177.2(ENSG00000255087):​n.707+3829G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,884 control chromosomes in the GnomAD database, including 13,400 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 0.40 (13400 hom., cov: 32)
• Consequence: ENSG00000255087 ENST00000530177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

Genes affected

ENSG00000255087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530177.2. 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
	ENSG00000255087	ENST00000530177.2	TSL:4	n.707+3829G>A		intron	N/A
	ENSG00000255087	ENST00000647195.1		n.696+3829G>A		intron	N/A
	ENSG00000255087	ENST00000654637.1		n.710+3829G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60769 AN: 151766 Hom.: 13372 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.401 AC: 60853 AN: 151884 Hom.: 13400 Cov.: 32 AF XY: 0.404 AC XY: 29998 AN XY: 74252

African (AFR) AF: 0.595 AC: 24611 AN: 41394

American (AMR) AF: 0.345 AC: 5264 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1282 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1888 AN: 5142

South Asian (SAS) AF: 0.325 AC: 1563 AN: 4810

European-Finnish (FIN) AF: 0.388 AC: 4097 AN: 10552

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21030 AN: 67944

Other (OTH) AF: 0.363 AC: 768 AN: 2114

Alfa AF: 0.363 Hom.: 1351

Bravo AF: 0.406

Asia WGS AF: 0.329 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.033
DANN	Benign	0.78
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs674237; hg19: chr11-126927412;