11-13276378-A-G

Variant names:

• chr11-13276378-A-G
• rs4757138
• ENST00000702886.2:n.*167T>C

Variant summary

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

The ENST00000702886.2(ENSG00000290083):​n.*167T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,072 control chromosomes in the GnomAD database, including 30,091 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 0.62 (30091 hom., cov: 32)
• Consequence: ENSG00000290083 ENST00000702886.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 18 publications found

Genes affected

ENSG00000290083 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702886.2. 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
	ENSG00000290083	ENST00000702886.2		n.*167T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94157 AN: 151954 Hom.: 30058 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.620 AC: 94243 AN: 152072 Hom.: 30091 Cov.: 32 AF XY: 0.622 AC XY: 46242 AN XY: 74322

African (AFR) AF: 0.463 AC: 19200 AN: 41478

American (AMR) AF: 0.618 AC: 9449 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2283 AN: 3470

East Asian (EAS) AF: 0.535 AC: 2771 AN: 5178

South Asian (SAS) AF: 0.638 AC: 3071 AN: 4810

European-Finnish (FIN) AF: 0.723 AC: 7637 AN: 10558

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47747 AN: 67972

Other (OTH) AF: 0.640 AC: 1355 AN: 2116

Alfa AF: 0.685 Hom.: 22315

Bravo AF: 0.607

Asia WGS AF: 0.605 AC: 2103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.25
PhyloP100		0.14
PromoterAI		-0.013	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4757138; hg19: chr11-13297925;