4-5002185-A-G

Variant names:

• chr4-5002185-A-G
• rs13117014
• ENST00000774609.1:n.268-2360A>G

Variant summary

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

The ENST00000774609.1(ENSG00000300857):​n.268-2360A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,666 control chromosomes in the GnomAD database, including 12,382 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 0.40 (12382 hom., cov: 32)
• Consequence: ENSG00000300857 ENST00000774609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 2 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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.268-2360A>G		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60583 AN: 151548 Hom.: 12343 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.400 AC: 60680 AN: 151666 Hom.: 12382 Cov.: 32 AF XY: 0.404 AC XY: 29911 AN XY: 74106

African (AFR) AF: 0.493 AC: 20362 AN: 41324

American (AMR) AF: 0.411 AC: 6282 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3466

East Asian (EAS) AF: 0.463 AC: 2374 AN: 5130

South Asian (SAS) AF: 0.492 AC: 2360 AN: 4796

European-Finnish (FIN) AF: 0.373 AC: 3928 AN: 10526

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.339 AC: 22985 AN: 67848

Other (OTH) AF: 0.404 AC: 850 AN: 2102

Alfa AF: 0.370 Hom.: 2297

Bravo AF: 0.406

Asia WGS AF: 0.470 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.89
DANN	Benign	0.34
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs13117014; hg19: chr4-5003912;