rs10111769

Variant names:

• chr8-21101245-T-C
• rs10111769
• ENST00000657283.1:n.2094+7589A>G

Variant summary

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

The ENST00000657283.1(ENSG00000254092):​n.2094+7589A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,106 control chromosomes in the GnomAD database, including 8,284 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 0.33 (8284 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000657283.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

ENSG00000254092 (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 = 0.507 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
ENSG00000254092	ENST00000657283.1	n.2094+7589A>G		intron_variant	Intron 2 of 3
ENSG00000254092	ENST00000657734.1	n.1327-41310A>G		intron_variant	Intron 2 of 4
ENSG00000254092	ENST00000659453.1	n.1640-41310A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49461 AN: 151988 Hom.: 8266 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.326 AC: 49520 AN: 152106 Hom.: 8284 Cov.: 32 AF XY: 0.330 AC XY: 24520 AN XY: 74366

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.332

Alfa AF: 0.311 Hom.: 3511

Bravo AF: 0.325

Asia WGS AF: 0.427 AC: 1485 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	0.90
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10111769; hg19: chr8-20958756;