10-59620724-C-G

Variant names:

• chr10-59620724-C-G
• rs10826334
• ENST00000644636.1:n.101-1398C>G

Variant summary

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

The ENST00000644636.1(ENSG00000235140):​n.101-1398C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0858 in 152,122 control chromosomes in the GnomAD database, including 739 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 (739 hom., cov: 33)
• Consequence: ENSG00000235140 ENST00000644636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 6 publications found

Genes affected

ENSG00000235140 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 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
ENSG00000235140	ENST00000644636.1	n.101-1398C>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13045 AN: 152004 Hom.: 737 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0578

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0659

Gnomad OTH AF: 0.0800

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

GnomAD4 genome AF: 0.0858 AC: 13057 AN: 152122 Hom.: 739 Cov.: 33 AF XY: 0.0832 AC XY: 6184 AN XY: 74366

African (AFR) AF: 0.159 AC: 6595 AN: 41458

American (AMR) AF: 0.0667 AC: 1019 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5178

South Asian (SAS) AF: 0.0574 AC: 277 AN: 4824

European-Finnish (FIN) AF: 0.0289 AC: 306 AN: 10604

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4476 AN: 67994

Other (OTH) AF: 0.0796 AC: 168 AN: 2110

Alfa AF: 0.0132 Hom.: 8

Bravo AF: 0.0916

Asia WGS AF: 0.0400 AC: 138 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs10826334; hg19: chr10-61380482;