rs10826964

Variant names:

• chr10-31568824-G-A
• rs10826964
• ENST00000829893.1:n.311-17208C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-31568824-G-A
• chr10-31568824-G-T

Variant summary

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

The ENST00000829893.1(ENSG00000307931):​n.311-17208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,130 control chromosomes in the GnomAD database, including 9,223 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 0.23 (9223 hom., cov: 32)
• Consequence: ENSG00000307931 ENST00000829893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 1 publications found

Genes affected

ENSG00000307931 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829893.1. 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
	ENSG00000307931	ENST00000829893.1		n.311-17208C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35288 AN: 152012 Hom.: 9189 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.232 AC: 35370 AN: 152130 Hom.: 9223 Cov.: 32 AF XY: 0.229 AC XY: 17064 AN XY: 74372

African (AFR) AF: 0.646 AC: 26776 AN: 41464

American (AMR) AF: 0.133 AC: 2037 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3470

East Asian (EAS) AF: 0.167 AC: 864 AN: 5172

South Asian (SAS) AF: 0.148 AC: 715 AN: 4816

European-Finnish (FIN) AF: 0.0720 AC: 764 AN: 10604

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3572 AN: 68006

Other (OTH) AF: 0.180 AC: 381 AN: 2114

Alfa AF: 0.109 Hom.: 631

Bravo AF: 0.257

Asia WGS AF: 0.162 AC: 564 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.45
PhyloP100		-0.33

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: rs10826964;

hg19: chr10-31857752;