rs10853181

Variant names:

• chr17-27812592-G-A
• rs10853181
• ENST00000582441.1:c.220-8251C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-27812592-G-A
• chr17-27812592-G-T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-8251C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,058 control chromosomes in the GnomAD database, including 24,874 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 0.55 (24874 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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
ENSG00000266202	ENST00000582441.1	c.220-8251C>T		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84233 AN: 151940 Hom.: 24870 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.554 AC: 84267 AN: 152058 Hom.: 24874 Cov.: 32 AF XY: 0.559 AC XY: 41550 AN XY: 74310

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.578

Alfa AF: 0.594 Hom.: 11158

Bravo AF: 0.544

Asia WGS AF: 0.682 AC: 2371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.085
DANN	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10853181; hg19: chr17-26139618;