19-41776424-G-T

Variant names:

• chr19-41776424-G-T
• rs10416839
• ENST00000601409.1:n.383+10087C>A

Variant summary

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

The ENST00000601409.1(ENSG00000268833):​n.383+10087C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,344 control chromosomes in the GnomAD database, including 6,173 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 0.27 (6173 hom., cov: 29)
• Consequence: ENSG00000268833 ENST00000601409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 9 publications found

Genes affected

ENSG00000268833 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=1.086).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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
ENSG00000268833	ENST00000601409.1	n.383+10087C>A		intron_variant	Intron 1 of 1	4
ENSG00000268833	ENST00000819470.1	n.111-18343C>A		intron_variant	Intron 1 of 1
ENSG00000306605	ENST00000819626.1	n.67-1096C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40274 AN: 151226 Hom.: 6177 Cov.: 29

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.266 AC: 40263 AN: 151344 Hom.: 6173 Cov.: 29 AF XY: 0.266 AC XY: 19626 AN XY: 73894

African (AFR) AF: 0.119 AC: 4902 AN: 41272

American (AMR) AF: 0.242 AC: 3687 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1440 AN: 3464

East Asian (EAS) AF: 0.246 AC: 1267 AN: 5150

South Asian (SAS) AF: 0.270 AC: 1297 AN: 4798

European-Finnish (FIN) AF: 0.321 AC: 3313 AN: 10326

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23192 AN: 67790

Other (OTH) AF: 0.288 AC: 604 AN: 2100

Alfa AF: 0.318 Hom.: 18390

Bravo AF: 0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.1
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs10416839; hg19: -;