rs10793057

Variant names:

• chr11-73257615-G-A
• rs10793057
• ENST00000832587.1:n.170-6691C>T

Variant summary

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

The ENST00000832587.1(ENSG00000308221):​n.170-6691C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 152,234 control chromosomes in the GnomAD database, including 950 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 0.086 (950 hom., cov: 32)
• Consequence: ENSG00000308221 ENST00000832587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 1 publications found

Genes affected

ENSG00000308221 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832587.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308221	ENST00000832587.1		n.170-6691C>T		intron	N/A
	ENSG00000308241	ENST00000832738.1		n.607-386G>A		intron	N/A
	ENSG00000308241	ENST00000832739.1		n.392-386G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0855 AC: 13004 AN: 152116 Hom.: 945 Cov.: 32

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0672

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0808

Gnomad OTH AF: 0.0815

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

GnomAD4 genome AF: 0.0855 AC: 13016 AN: 152234 Hom.: 950 Cov.: 32 AF XY: 0.0907 AC XY: 6751 AN XY: 74418

African (AFR) AF: 0.0207 AC: 860 AN: 41574

American (AMR) AF: 0.189 AC: 2884 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0672 AC: 233 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1516 AN: 5162

South Asian (SAS) AF: 0.182 AC: 880 AN: 4824

European-Finnish (FIN) AF: 0.0906 AC: 960 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0807 AC: 5491 AN: 68006

Other (OTH) AF: 0.0825 AC: 174 AN: 2108

Alfa AF: 0.0859 Hom.: 1265

Bravo AF: 0.0881

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.45
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs10793057; hg19: chr11-72968660;