11-128279170-G-A

Variant names:

• chr11-128279170-G-A
• rs722345
• ENST00000827095.1:n.444+17267G>A

Variant summary

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

The ENST00000827095.1(ENSG00000289398):​n.444+17267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,848 control chromosomes in the GnomAD database, including 8,058 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 0.30 (8058 hom., cov: 30)
• Consequence: ENSG00000289398 ENST00000827095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 3 publications found

Genes affected

ENSG00000289398 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827095.1. 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
	ENSG00000289398	ENST00000827095.1		n.444+17267G>A		intron	N/A
	ENSG00000289398	ENST00000827096.1		n.315+16074G>A		intron	N/A
	ENSG00000289398	ENST00000827097.1		n.39-8746G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46319 AN: 151730 Hom.: 8062 Cov.: 30

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.305 AC: 46307 AN: 151848 Hom.: 8058 Cov.: 30 AF XY: 0.298 AC XY: 22078 AN XY: 74206

African (AFR) AF: 0.160 AC: 6642 AN: 41426

American (AMR) AF: 0.237 AC: 3616 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3466

East Asian (EAS) AF: 0.0643 AC: 332 AN: 5162

South Asian (SAS) AF: 0.261 AC: 1253 AN: 4798

European-Finnish (FIN) AF: 0.350 AC: 3684 AN: 10514

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28263 AN: 67914

Other (OTH) AF: 0.309 AC: 651 AN: 2110

Alfa AF: 0.351 Hom.: 3977

Bravo AF: 0.290

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.2
DANN	Benign	0.94
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs722345; hg19: chr11-128149065;