10-58833982-C-T

Variant names:

• chr10-58833982-C-T
• rs7085810
• ENST00000783190.1:n.210-14020G>A

Variant summary

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

The ENST00000783190.1(ENSG00000301981):​n.210-14020G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,016 control chromosomes in the GnomAD database, including 49,550 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 0.78 (49550 hom., cov: 31)
• Consequence: ENSG00000301981 ENST00000783190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 2 publications found

Genes affected

ENSG00000301981 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301981	ENST00000783190.1	n.210-14020G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118796 AN: 151898 Hom.: 49543 Cov.: 31

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.782 AC: 118828 AN: 152016 Hom.: 49550 Cov.: 31 AF XY: 0.782 AC XY: 58094 AN XY: 74320

African (AFR) AF: 0.462 AC: 19124 AN: 41396

American (AMR) AF: 0.883 AC: 13495 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3361 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4475 AN: 5164

South Asian (SAS) AF: 0.821 AC: 3949 AN: 4810

European-Finnish (FIN) AF: 0.846 AC: 8948 AN: 10582

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62634 AN: 68002

Other (OTH) AF: 0.800 AC: 1683 AN: 2104

Alfa AF: 0.882 Hom.: 26724

Bravo AF: 0.771

Asia WGS AF: 0.794 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.0
DANN	Benign	0.63
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7085810; hg19: chr10-60593742;