rs11137379

Variant names:

• chr9-138133487-G-A
• rs11137379
• ENST00000776045.1:n.236-4929G>A

Variant summary

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

The ENST00000776045.1(ENSG00000301083):​n.236-4929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 150,858 control chromosomes in the GnomAD database, including 3,339 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 0.17 (3339 hom., cov: 31)
• Consequence: ENSG00000301083 ENST00000776045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 3 publications found

Genes affected

ENSG00000301083 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301083	ENST00000776045.1	n.236-4929G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25434 AN: 150740 Hom.: 3339 Cov.: 31

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.169 AC: 25424 AN: 150858 Hom.: 3339 Cov.: 31 AF XY: 0.163 AC XY: 12027 AN XY: 73726

African (AFR) AF: 0.0584 AC: 2419 AN: 41406

American (AMR) AF: 0.178 AC: 2708 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1172 AN: 3446

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5172

South Asian (SAS) AF: 0.0984 AC: 469 AN: 4764

European-Finnish (FIN) AF: 0.159 AC: 1663 AN: 10440

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.240 AC: 16108 AN: 67162

Other (OTH) AF: 0.209 AC: 434 AN: 2076

Alfa AF: 0.224 Hom.: 5718

Bravo AF: 0.170

Asia WGS AF: 0.0490 AC: 172 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.5
DANN	Benign	0.53
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs11137379; hg19: chr9-141027939;