rs10503354

Variant names:

• chr8-6095422-G-A
• rs10503354
• ENST00000519555.1:n.250+4906C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-6095422-G-A
• chr8-6095422-G-C

Variant summary

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

The ENST00000519555.1(ENSG00000253880):​n.250+4906C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,090 control chromosomes in the GnomAD database, including 2,392 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 0.18 (2392 hom., cov: 33)
• Consequence: ENSG00000253880 ENST00000519555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

Genes affected

ENSG00000253880 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 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
ENSG00000253880	ENST00000519555.1	n.250+4906C>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26750 AN: 151972 Hom.: 2390 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.176 AC: 26767 AN: 152090 Hom.: 2392 Cov.: 33 AF XY: 0.180 AC XY: 13374 AN XY: 74344

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.163

Alfa AF: 0.151 Hom.: 3756

Bravo AF: 0.181

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503354; hg19: chr8-5952944;