rs10510263

Variant names:

• chr3-3479127-T-C
• rs10510263
• ENST00000420000.6:n.201-96477A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-3479127-T-C
• chr3-3479127-T-G

Variant summary

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

The ENST00000455703.1(ENSG00000223727):​n.59+4912A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0248 in 152,160 control chromosomes in the GnomAD database, including 262 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 0.025 (262 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000455703.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 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
ENSG00000223727	ENST00000420000.6	n.201-96477A>G		intron_variant	Intron 2 of 4	4
ENSG00000223727	ENST00000451031.5	n.77+4912A>G		intron_variant	Intron 1 of 5	3
ENSG00000223727	ENST00000455703.1	n.59+4912A>G		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0249 AC: 3780 AN: 152042 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.00369

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00899

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.0375

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0170

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0248 AC: 3769 AN: 152160 Hom.: 262 Cov.: 32 AF XY: 0.0281 AC XY: 2089 AN XY: 74416

Gnomad4 AFR AF: 0.00368

Gnomad4 AMR AF: 0.00898

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.0714

Gnomad4 FIN AF: 0.0375

Gnomad4 NFE AF: 0.0170

Gnomad4 OTH AF: 0.0189

Alfa AF: 0.0186 Hom.: 9

Bravo AF: 0.0225

Asia WGS AF: 0.141 AC: 489 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510263; hg19: chr3-3520811;