rs10510257

Variant names:

• chr3-3304454-G-A
• rs10510257
• ENST00000420000.6:n.537+32846C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-3304454-G-A
• chr3-3304454-G-T

Variant summary

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

The ENST00000451031.5(ENSG00000223727):​n.339+32846C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,896 control chromosomes in the GnomAD database, including 3,848 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 0.22 (3848 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000451031.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

ENSG00000223727 (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 (SAS) allele frequency at 95% confidence interval = 0.239 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.537+32846C>T		intron_variant	Intron 4 of 4	4
ENSG00000223727	ENST00000451031.5	n.339+32846C>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33673 AN: 151780 Hom.: 3840 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.222 AC: 33700 AN: 151896 Hom.: 3848 Cov.: 32 AF XY: 0.221 AC XY: 16404 AN XY: 74192

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.239

Alfa AF: 0.219 Hom.: 2566

Bravo AF: 0.223

Asia WGS AF: 0.200 AC: 698 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	2.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510257; hg19: chr3-3346138;