ENST00000832587.1:n.170-6691C>T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369382	XR_950296.3	n.163-386G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308221	ENST00000832587.1	n.170-6691C>T		intron_variant	Intron 1 of 2
ENSG00000308241	ENST00000832738.1	n.607-386G>A		intron_variant	Intron 5 of 5
ENSG00000308241	ENST00000832739.1	n.392-386G>A		intron_variant	Intron 4 of 4

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 v4.3

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;