rs10886971

Variant names:

• chr10-83714375-C-T
• rs10886971
• ENST00000659573.2:n.235-3500G>A

Variant summary

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

The ENST00000659573.2(ENSG00000286876):​n.235-3500G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,074 control chromosomes in the GnomAD database, including 1,393 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 0.10 (1393 hom., cov: 33)
• Consequence: ENSG00000286876 ENST00000659573.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 1 publications found

Genes affected

ENSG00000286876 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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
ENSG00000286876	ENST00000659573.2	n.235-3500G>A		intron_variant	Intron 2 of 2
ENSG00000286876	ENST00000789038.1	n.188-3500G>A		intron_variant	Intron 2 of 2
ENSG00000286876	ENST00000789039.1	n.384-3500G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15666 AN: 151956 Hom.: 1392 Cov.: 33

Gnomad AFR AF: 0.0243

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.103 AC: 15650 AN: 152074 Hom.: 1393 Cov.: 33 AF XY: 0.110 AC XY: 8167 AN XY: 74340

African (AFR) AF: 0.0243 AC: 1009 AN: 41534

American (AMR) AF: 0.121 AC: 1853 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2581 AN: 5158

South Asian (SAS) AF: 0.202 AC: 976 AN: 4820

European-Finnish (FIN) AF: 0.159 AC: 1675 AN: 10556

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6762 AN: 67948

Other (OTH) AF: 0.114 AC: 241 AN: 2108

Alfa AF: 0.0900 Hom.: 78

Bravo AF: 0.100

Asia WGS AF: 0.278 AC: 964 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.62
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs10886971; hg19: chr10-85474131;