10-20521596-T-G

Variant names:

• chr10-20521596-T-G
• rs16920624
• ENST00000785943.1:n.367+5826T>G

Variant summary

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

The ENST00000785943.1(ENSG00000302338):​n.367+5826T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0967 in 152,180 control chromosomes in the GnomAD database, including 1,071 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 0.097 (1071 hom., cov: 32)
• Consequence: ENSG00000302338 ENST00000785943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 12 publications found

Genes affected

ENSG00000302338 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 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
ENSG00000302338	ENST00000785943.1	n.367+5826T>G		intron_variant	Intron 2 of 5
ENSG00000302338	ENST00000785944.1	n.280+5826T>G		intron_variant	Intron 2 of 3
ENSG00000302338	ENST00000785945.1	n.214+5826T>G		intron_variant	Intron 2 of 4
ENSG00000302338	ENST00000785947.1	n.123+5826T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0967 AC: 14711 AN: 152062 Hom.: 1072 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0280

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0601

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0967 AC: 14723 AN: 152180 Hom.: 1071 Cov.: 32 AF XY: 0.0947 AC XY: 7043 AN XY: 74408

African (AFR) AF: 0.186 AC: 7704 AN: 41510

American (AMR) AF: 0.0673 AC: 1026 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5176

South Asian (SAS) AF: 0.119 AC: 577 AN: 4830

European-Finnish (FIN) AF: 0.0280 AC: 297 AN: 10624

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0602 AC: 4092 AN: 67998

Other (OTH) AF: 0.109 AC: 230 AN: 2114

Alfa AF: 0.0785 Hom.: 1932

Bravo AF: 0.105

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.35
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs16920624; hg19: chr10-20810525;