rs3026719

Variant names:

• chr10-43067919-C-T
• rs3026719
• ENST00000794440.1:n.257+3387G>A

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.257+3387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.063 in 152,272 control chromosomes in the GnomAD database, including 495 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 0.063 (495 hom., cov: 34)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 0 publications found

Genes affected

ENSG00000303432 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0831 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794440.1. 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
	ENSG00000303432	ENST00000794440.1		n.257+3387G>A		intron	N/A
	ENSG00000303432	ENST00000794441.1		n.323-68G>A		intron	N/A
	ENSG00000303432	ENST00000794442.1		n.314-34G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0631 AC: 9600 AN: 152154 Hom.: 495 Cov.: 34

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0630 AC: 9597 AN: 152272 Hom.: 495 Cov.: 34 AF XY: 0.0660 AC XY: 4916 AN XY: 74458

African (AFR) AF: 0.0141 AC: 585 AN: 41564

American (AMR) AF: 0.0416 AC: 637 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 366 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0247 AC: 119 AN: 4822

European-Finnish (FIN) AF: 0.178 AC: 1884 AN: 10610

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0849 AC: 5777 AN: 68018

Other (OTH) AF: 0.0582 AC: 123 AN: 2114

Alfa AF: 0.0706 Hom.: 60

Bravo AF: 0.0517

Asia WGS AF: 0.00982 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.91
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs3026719; hg19: chr10-43563367;