rs10490889

Variant names:

• chr3-6240341-G-A
• rs10490889
• ENST00000435651.1:n.95+91763G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435651.1(ENSG00000226022):​n.95+91763G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,012 control chromosomes in the GnomAD database, including 8,989 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 0.34 (8989 hom., cov: 33)
• Consequence: ENSG00000226022 ENST00000435651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

ENSG00000226022 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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
ENSG00000226022	ENST00000435651.1	n.95+91763G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50938 AN: 151894 Hom.: 8981 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.335 AC: 50986 AN: 152012 Hom.: 8989 Cov.: 33 AF XY: 0.337 AC XY: 25010 AN XY: 74298

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.313

Alfa AF: 0.347 Hom.: 1603

Bravo AF: 0.325

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490889; hg19: chr3-6282028;