rs10402233

Variant names:

• chr19-35289948-A-G
• rs10402233
• ENST00000827558.1:n.391+3134T>C

Variant summary

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

The ENST00000827558.1(ENSG00000307628):​n.391+3134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,912 control chromosomes in the GnomAD database, including 11,165 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 0.38 (11165 hom., cov: 31)
• Consequence: ENSG00000307628 ENST00000827558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 6 publications found

Genes affected

ENSG00000307628 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 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
ENSG00000307628	ENST00000827558.1	n.391+3134T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57980 AN: 151794 Hom.: 11168 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.382 AC: 58009 AN: 151912 Hom.: 11165 Cov.: 31 AF XY: 0.381 AC XY: 28304 AN XY: 74232

African (AFR) AF: 0.407 AC: 16862 AN: 41430

American (AMR) AF: 0.381 AC: 5806 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1316 AN: 3450

East Asian (EAS) AF: 0.261 AC: 1348 AN: 5174

South Asian (SAS) AF: 0.457 AC: 2201 AN: 4816

European-Finnish (FIN) AF: 0.367 AC: 3864 AN: 10534

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25242 AN: 67954

Other (OTH) AF: 0.410 AC: 861 AN: 2102

Alfa AF: 0.377 Hom.: 18475

Bravo AF: 0.380

Asia WGS AF: 0.378 AC: 1314 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.58
DANN	Benign	0.79
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs10402233; hg19: chr19-35780851;