ENST00000774609.1:n.356+2906A>G

Variant names:

• chr4-5007539-A-G
• rs12171324
• ENST00000774609.1:n.356+2906A>G

Variant summary

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

The ENST00000774609.1(ENSG00000300857):​n.356+2906A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,774 control chromosomes in the GnomAD database, including 16,211 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 0.45 (16211 hom., cov: 31)
• Consequence: ENSG00000300857 ENST00000774609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 1 publications found

Genes affected

ENSG00000300857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 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
ENSG00000300857	ENST00000774609.1	n.356+2906A>G		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68894 AN: 151656 Hom.: 16174 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.454 AC: 68976 AN: 151774 Hom.: 16211 Cov.: 31 AF XY: 0.462 AC XY: 34281 AN XY: 74142

African (AFR) AF: 0.343 AC: 14198 AN: 41366

American (AMR) AF: 0.547 AC: 8359 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1539 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3132 AN: 5116

South Asian (SAS) AF: 0.483 AC: 2322 AN: 4804

European-Finnish (FIN) AF: 0.576 AC: 6051 AN: 10512

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31954 AN: 67926

Other (OTH) AF: 0.433 AC: 910 AN: 2102

Alfa AF: 0.464 Hom.: 5586

Bravo AF: 0.445

Asia WGS AF: 0.540 AC: 1878 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.46
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs12171324; hg19: chr4-5009266;