rs10885211

Variant names:

• chr10-111564544-C-T
• rs10885211
• ENST00000829409.1:n.117-62868G>A

Variant summary

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

The ENST00000829409.1(ENSG00000307856):​n.117-62868G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,040 control chromosomes in the GnomAD database, including 20,577 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 0.51 (20577 hom., cov: 32)
• Consequence: ENSG00000307856 ENST00000829409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 2 publications found

Genes affected

ENSG00000307856 (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 (AFR) allele frequency at 95% confidence interval = 0.631 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
ENSG00000307856	ENST00000829409.1	n.117-62868G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77635 AN: 151922 Hom.: 20551 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.511 AC: 77693 AN: 152040 Hom.: 20577 Cov.: 32 AF XY: 0.508 AC XY: 37780 AN XY: 74316

African (AFR) AF: 0.637 AC: 26433 AN: 41474

American (AMR) AF: 0.398 AC: 6073 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2004 AN: 3472

East Asian (EAS) AF: 0.297 AC: 1531 AN: 5162

South Asian (SAS) AF: 0.499 AC: 2405 AN: 4824

European-Finnish (FIN) AF: 0.498 AC: 5260 AN: 10562

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32431 AN: 67962

Other (OTH) AF: 0.510 AC: 1078 AN: 2114

Alfa AF: 0.487 Hom.: 3271

Bravo AF: 0.506

Asia WGS AF: 0.390 AC: 1361 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	1.3
DANN	Benign	0.46
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs10885211; hg19: chr10-113324302;