4-20049110-G-A

Variant names:

• chr4-20049110-G-A
• rs901123
• ENST00000819692.1:n.598-8390G>A

Variant summary

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

The ENST00000819692.1(ENSG00000306609):​n.598-8390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,762 control chromosomes in the GnomAD database, including 11,947 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 0.39 (11947 hom., cov: 31)
• Consequence: ENSG00000306609 ENST00000819692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 2 publications found

Genes affected

ENSG00000306609 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819692.1. 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
	ENSG00000306609	ENST00000819692.1		n.598-8390G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59366 AN: 151646 Hom.: 11930 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.391 AC: 59413 AN: 151762 Hom.: 11947 Cov.: 31 AF XY: 0.388 AC XY: 28742 AN XY: 74154

African (AFR) AF: 0.486 AC: 20117 AN: 41356

American (AMR) AF: 0.413 AC: 6293 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3466

East Asian (EAS) AF: 0.361 AC: 1853 AN: 5126

South Asian (SAS) AF: 0.318 AC: 1524 AN: 4798

European-Finnish (FIN) AF: 0.355 AC: 3752 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23261 AN: 67904

Other (OTH) AF: 0.379 AC: 799 AN: 2108

Alfa AF: 0.352 Hom.: 13374

Bravo AF: 0.402

Asia WGS AF: 0.409 AC: 1422 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.45
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs901123; hg19: chr4-20050733;