rs10826304

Variant names:

• chr10-59510907-G-A
• rs10826304
• ENST00000796729.1:n.106+27807C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-59510907-G-A
• chr10-59510907-G-C

Variant summary

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

The ENST00000796729.1(ENSG00000303721):​n.106+27807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,026 control chromosomes in the GnomAD database, including 13,317 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 0.40 (13317 hom., cov: 32)
• Consequence: ENSG00000303721 ENST00000796729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 1 publications found

Genes affected

ENSG00000303721 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796729.1. 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
	ENSG00000303721	ENST00000796729.1		n.106+27807C>T		intron	N/A
	ENSG00000303721	ENST00000796730.1		n.219+11668C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60263 AN: 151908 Hom.: 13323 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.396 AC: 60260 AN: 152026 Hom.: 13317 Cov.: 32 AF XY: 0.398 AC XY: 29562 AN XY: 74278

African (AFR) AF: 0.194 AC: 8066 AN: 41482

American (AMR) AF: 0.369 AC: 5632 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1858 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2816 AN: 5168

South Asian (SAS) AF: 0.446 AC: 2152 AN: 4828

European-Finnish (FIN) AF: 0.463 AC: 4875 AN: 10520

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33252 AN: 67960

Other (OTH) AF: 0.451 AC: 954 AN: 2116

Alfa AF: 0.333 Hom.: 1457

Bravo AF: 0.380

Asia WGS AF: 0.431 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		0.38

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: rs10826304;

hg19: chr10-61270665;

COSMIC: COSV56522401;