19-39240115-A-T

Variant names:

• chr19-39240115-A-T
• rs35790907
• ENST00000735578.1:n.116-3121A>T

Variant summary

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

The ENST00000735578.1(ENSG00000296032):​n.116-3121A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,772 control chromosomes in the GnomAD database, including 14,179 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 (14179 hom., cov: 31)
• Consequence: ENSG00000296032 ENST00000735578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 8 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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
ENSG00000296032	ENST00000735578.1	n.116-3121A>T		intron_variant	Intron 1 of 1
ENSG00000296032	ENST00000735579.1	n.90-3121A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59945 AN: 151654 Hom.: 14147 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.396 AC: 60032 AN: 151772 Hom.: 14179 Cov.: 31 AF XY: 0.387 AC XY: 28711 AN XY: 74196

African (AFR) AF: 0.660 AC: 27296 AN: 41382

American (AMR) AF: 0.381 AC: 5818 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3464

East Asian (EAS) AF: 0.0824 AC: 423 AN: 5136

South Asian (SAS) AF: 0.240 AC: 1155 AN: 4808

European-Finnish (FIN) AF: 0.228 AC: 2402 AN: 10544

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20358 AN: 67872

Other (OTH) AF: 0.368 AC: 776 AN: 2108

Alfa AF: 0.351 Hom.: 1267

Bravo AF: 0.419

Asia WGS AF: 0.203 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.43
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs35790907; hg19: chr19-39730755;