rs4939879

Variant names:

• chr18-49619613-A-G
• rs4939879
• ENST00000849192.1:n.231+6521A>G

Variant summary

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

The ENST00000849192.1(ENSG00000310339):​n.231+6521A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,934 control chromosomes in the GnomAD database, including 18,638 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 0.48 (18638 hom., cov: 32)
• Consequence: ENSG00000310339 ENST00000849192.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 5 publications found

Genes affected

ENSG00000310339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849192.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310339	ENST00000849192.1		n.231+6521A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73562 AN: 151816 Hom.: 18624 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.485 AC: 73619 AN: 151934 Hom.: 18638 Cov.: 32 AF XY: 0.489 AC XY: 36305 AN XY: 74224

African (AFR) AF: 0.348 AC: 14424 AN: 41452

American (AMR) AF: 0.554 AC: 8455 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1814 AN: 3464

East Asian (EAS) AF: 0.412 AC: 2117 AN: 5140

South Asian (SAS) AF: 0.507 AC: 2435 AN: 4806

European-Finnish (FIN) AF: 0.583 AC: 6152 AN: 10552

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36833 AN: 67942

Other (OTH) AF: 0.469 AC: 989 AN: 2108

Alfa AF: 0.524 Hom.: 28220

Bravo AF: 0.479

Asia WGS AF: 0.500 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.3
DANN	Benign	0.75
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs4939879; hg19: chr18-47145983;