11-127026628-A-G

Variant names:

• chr11-127026628-A-G
• rs642387
• ENST00000530177.2:n.154+4721A>G

Variant summary

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

The ENST00000530177.2(ENSG00000255087):​n.154+4721A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,886 control chromosomes in the GnomAD database, including 10,209 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 0.36 (10209 hom., cov: 32)
• Consequence: ENSG00000255087 ENST00000530177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255087	ENST00000530177.2	TSL:4	n.154+4721A>G		intron	N/A
	ENSG00000255087	ENST00000647195.1		n.143+4721A>G		intron	N/A
	ENSG00000255087	ENST00000654157.1		n.150+4721A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54001 AN: 151768 Hom.: 10197 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.356 AC: 54061 AN: 151886 Hom.: 10209 Cov.: 32 AF XY: 0.362 AC XY: 26862 AN XY: 74234

African (AFR) AF: 0.482 AC: 19939 AN: 41388

American (AMR) AF: 0.320 AC: 4880 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3468

East Asian (EAS) AF: 0.383 AC: 1976 AN: 5162

South Asian (SAS) AF: 0.327 AC: 1575 AN: 4810

European-Finnish (FIN) AF: 0.379 AC: 4003 AN: 10558

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19481 AN: 67942

Other (OTH) AF: 0.324 AC: 682 AN: 2106

Alfa AF: 0.309 Hom.: 2992

Bravo AF: 0.356

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.71

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs642387;

hg19: chr11-126896523;