11-128187588-C-T

Variant names:

• chr11-128187588-C-T
• rs476994
• ENST00000783239.1:n.271-3642G>A

Variant summary

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

The ENST00000783239.1(ENSG00000301990):​n.271-3642G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,066 control chromosomes in the GnomAD database, including 5,054 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 0.23 (5054 hom., cov: 32)
• Consequence: ENSG00000301990 ENST00000783239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 publications found

Genes affected

ENSG00000301990 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783239.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301990	ENST00000783239.1		n.271-3642G>A		intron	N/A
	ENSG00000301990	ENST00000783240.1		n.200-3642G>A		intron	N/A
	ENSG00000301990	ENST00000783243.1		n.278-3642G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35126 AN: 151948 Hom.: 5056 Cov.: 32

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.00732

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.231 AC: 35117 AN: 152066 Hom.: 5054 Cov.: 32 AF XY: 0.232 AC XY: 17247 AN XY: 74304

African (AFR) AF: 0.0855 AC: 3549 AN: 41494

American (AMR) AF: 0.200 AC: 3056 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1462 AN: 3466

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5180

South Asian (SAS) AF: 0.331 AC: 1594 AN: 4810

European-Finnish (FIN) AF: 0.352 AC: 3717 AN: 10562

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20735 AN: 67956

Other (OTH) AF: 0.277 AC: 585 AN: 2114

Alfa AF: 0.266 Hom.: 1502

Bravo AF: 0.210

Asia WGS AF: 0.180 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.99
DANN	Benign	0.60
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs476994; hg19: chr11-128057483;