rs958039

Variant names:

• chr19-39239661-T-A
• rs958039
• ENST00000735578.1:n.116-3575T>A

Variant summary

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

The ENST00000735578.1(ENSG00000296032):​n.116-3575T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,918 control chromosomes in the GnomAD database, including 10,464 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 0.36 (10464 hom., cov: 31)
• Consequence: ENSG00000296032 ENST00000735578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 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.116-3575T>A		intron	N/A
	ENSG00000296032	ENST00000735579.1		n.90-3575T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54139 AN: 151798 Hom.: 10441 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.357 AC: 54215 AN: 151918 Hom.: 10464 Cov.: 31 AF XY: 0.350 AC XY: 25946 AN XY: 74236

African (AFR) AF: 0.491 AC: 20334 AN: 41406

American (AMR) AF: 0.365 AC: 5561 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1415 AN: 3470

East Asian (EAS) AF: 0.0825 AC: 426 AN: 5164

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4810

European-Finnish (FIN) AF: 0.248 AC: 2625 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21578 AN: 67938

Other (OTH) AF: 0.340 AC: 717 AN: 2108

Alfa AF: 0.354 Hom.: 1215

Bravo AF: 0.372

Asia WGS AF: 0.201 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-0.84

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs958039;

hg19: chr19-39730301;