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. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455703.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223727	ENST00000420000.6	TSL:4	n.201-96477A>G		intron	N/A
	ENSG00000223727	ENST00000451031.5	TSL:3	n.77+4912A>G		intron	N/A
	ENSG00000223727	ENST00000455703.1	TSL:2	n.59+4912A>G		intron	N/A

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

African (AFR) AF: 0.00368 AC: 153 AN: 41558

American (AMR) AF: 0.00898 AC: 137 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1495 AN: 5174

South Asian (SAS) AF: 0.0714 AC: 345 AN: 4830

European-Finnish (FIN) AF: 0.0375 AC: 398 AN: 10612

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0170 AC: 1153 AN: 67934

Other (OTH) AF: 0.0189 AC: 40 AN: 2114

Alfa AF: 0.0120 Hom.: 176

Bravo AF: 0.0225

Asia WGS AF: 0.141 AC: 489 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.83
PhyloP100		0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10510263;

hg19: chr3-3520811;