rs10505127

Variant names:

• chr8-109041254-C-A
• rs10505127
• ENST00000522244.1:n.264+2423G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-109041254-C-A
• chr8-109041254-C-G

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.264+2423G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,030 control chromosomes in the GnomAD database, including 29,168 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 0.61 (29168 hom., cov: 32)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

ENSG00000253796 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 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
ENSG00000253796	ENST00000522244.1	n.264+2423G>T		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93385 AN: 151912 Hom.: 29132 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.615 AC: 93476 AN: 152030 Hom.: 29168 Cov.: 32 AF XY: 0.616 AC XY: 45796 AN XY: 74310

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.603

Alfa AF: 0.586 Hom.: 3283

Bravo AF: 0.634

Asia WGS AF: 0.668 AC: 2323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505127; hg19: chr8-110053483;