19-39207334-A-G

Variant names:

• chr19-39207334-A-G
• rs11083515
• ENST00000735578.1:n.115+4286A>G

Variant summary

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

The ENST00000735578.1(ENSG00000296032):​n.115+4286A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,818 control chromosomes in the GnomAD database, including 21,641 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 0.53 (21641 hom., cov: 30)
• Consequence: ENSG00000296032 ENST00000735578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 11 publications found

Genes affected

ENSG00000296032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000735578.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296032	ENST00000735578.1		n.115+4286A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80829 AN: 151700 Hom.: 21613 Cov.: 30

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.533 AC: 80897 AN: 151818 Hom.: 21641 Cov.: 30 AF XY: 0.531 AC XY: 39379 AN XY: 74180

African (AFR) AF: 0.570 AC: 23614 AN: 41392

American (AMR) AF: 0.501 AC: 7624 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3470

East Asian (EAS) AF: 0.511 AC: 2636 AN: 5162

South Asian (SAS) AF: 0.427 AC: 2051 AN: 4806

European-Finnish (FIN) AF: 0.514 AC: 5412 AN: 10524

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35802 AN: 67938

Other (OTH) AF: 0.533 AC: 1119 AN: 2100

Alfa AF: 0.527 Hom.: 94129

Bravo AF: 0.533

Asia WGS AF: 0.480 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.37
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11083515; hg19: chr19-39697974;