chr9-136374683-A-G

Variant names:

• chr9-136374683-A-G
• rs3812558
• ENST00000772719.1:n.1148A>G

Variant summary

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

The ENST00000772719.1(ENSG00000300558):​n.1148A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,090 control chromosomes in the GnomAD database, including 11,311 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 0.38 (11311 hom., cov: 33)
• Consequence: ENSG00000300558 ENST00000772719.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 23 publications found

Genes affected

ENSG00000300558 (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 (AMR) allele frequency at 95% confidence interval = 0.464 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
ENSG00000300558	ENST00000772719.1	n.1148A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57523 AN: 151972 Hom.: 11292 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.379 AC: 57593 AN: 152090 Hom.: 11311 Cov.: 33 AF XY: 0.377 AC XY: 28042 AN XY: 74334

African (AFR) AF: 0.288 AC: 11945 AN: 41494

American (AMR) AF: 0.473 AC: 7231 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1602 AN: 5158

South Asian (SAS) AF: 0.330 AC: 1590 AN: 4822

European-Finnish (FIN) AF: 0.413 AC: 4361 AN: 10564

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28439 AN: 67962

Other (OTH) AF: 0.355 AC: 752 AN: 2116

Alfa AF: 0.414 Hom.: 2174

Bravo AF: 0.375

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs3812558; hg19: chr9-139269135;