10-58833163-C-T

Variant names:

• chr10-58833163-C-T
• rs6481440
• ENST00000783190.1:n.210-13201G>A

Variant summary

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

The ENST00000783190.1(ENSG00000301981):​n.210-13201G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,186 control chromosomes in the GnomAD database, including 61,555 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 0.90 (61555 hom., cov: 31)
• Consequence: ENSG00000301981 ENST00000783190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 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.210-13201G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136530 AN: 152068 Hom.: 61506 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.898 AC: 136639 AN: 152186 Hom.: 61555 Cov.: 31 AF XY: 0.896 AC XY: 66656 AN XY: 74396

African (AFR) AF: 0.820 AC: 34032 AN: 41508

American (AMR) AF: 0.933 AC: 14264 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3387 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4603 AN: 5164

South Asian (SAS) AF: 0.881 AC: 4242 AN: 4816

European-Finnish (FIN) AF: 0.880 AC: 9317 AN: 10586

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63718 AN: 68032

Other (OTH) AF: 0.900 AC: 1902 AN: 2114

Alfa AF: 0.911 Hom.: 8175

Bravo AF: 0.899

Asia WGS AF: 0.880 AC: 3064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.47
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs6481440; hg19: chr10-60592923;