rs10886106

Variant names:

• chr10-117633143-A-C
• rs10886106
• ENST00000806653.1:n.92+22311A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-117633143-A-C
• chr10-117633143-A-G
• chr10-117633143-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000806653.1(ENSG00000304858):​n.92+22311A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,118 control chromosomes in the GnomAD database, including 3,738 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 0.21 (3738 hom., cov: 32)
• Consequence: ENSG00000304858 ENST00000806653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 0 publications found

Genes affected

ENSG00000304858 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.292 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
ENSG00000304858	ENST00000806653.1	n.92+22311A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32543 AN: 152000 Hom.: 3719 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.214 AC: 32607 AN: 152118 Hom.: 3738 Cov.: 32 AF XY: 0.220 AC XY: 16350 AN XY: 74352

African (AFR) AF: 0.223 AC: 9240 AN: 41494

American (AMR) AF: 0.299 AC: 4578 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1062 AN: 5176

South Asian (SAS) AF: 0.147 AC: 711 AN: 4824

European-Finnish (FIN) AF: 0.271 AC: 2863 AN: 10558

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13174 AN: 67992

Other (OTH) AF: 0.191 AC: 402 AN: 2110

Alfa AF: 0.173 Hom.: 1269

Bravo AF: 0.218

Asia WGS AF: 0.209 AC: 728 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	8.2
DANN	Benign	0.28
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10886106; hg19: chr10-119392654;