rs10883688

Variant names:

• chr10-101750636-A-C
• rs10883688
• ENST00000785080.1:n.164-6419T>G

Variant summary

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

The ENST00000785080.1(ENSG00000302227):​n.164-6419T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,678 control chromosomes in the GnomAD database, including 16,602 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 0.45 (16602 hom., cov: 29)
• Consequence: ENSG00000302227 ENST00000785080.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801
• Publications: 4 publications found

Genes affected

ENSG00000302227 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785080.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302227	ENST00000785080.1		n.164-6419T>G		intron	N/A
	ENSG00000302227	ENST00000785081.1		n.162-6419T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68379 AN: 151560 Hom.: 16590 Cov.: 29

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.451 AC: 68408 AN: 151678 Hom.: 16602 Cov.: 29 AF XY: 0.452 AC XY: 33541 AN XY: 74124

African (AFR) AF: 0.260 AC: 10758 AN: 41350

American (AMR) AF: 0.492 AC: 7504 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1896 AN: 3466

East Asian (EAS) AF: 0.753 AC: 3895 AN: 5172

South Asian (SAS) AF: 0.383 AC: 1836 AN: 4800

European-Finnish (FIN) AF: 0.476 AC: 4977 AN: 10458

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35857 AN: 67862

Other (OTH) AF: 0.477 AC: 1007 AN: 2112

Alfa AF: 0.483 Hom.: 6990

Bravo AF: 0.446

Asia WGS AF: 0.510 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.8
DANN	Benign	0.84
PhyloP100		0.80

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10883688;

hg19: chr10-103510393;