rs10444517

Variant names:

• chr12-93957047-C-T
• rs10444517
• ENST00000786429.1:n.196+39285G>A

Variant summary

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

The ENST00000786429.1(ENSG00000257283):​n.196+39285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0879 in 152,212 control chromosomes in the GnomAD database, including 654 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 0.088 (654 hom., cov: 32)
• Consequence: ENSG00000257283 ENST00000786429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682
• Publications: 2 publications found

Genes affected

ENSG00000257283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 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
ENSG00000257283	ENST00000786429.1	n.196+39285G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0880 AC: 13379 AN: 152094 Hom.: 653 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0683

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

GnomAD4 genome AF: 0.0879 AC: 13383 AN: 152212 Hom.: 654 Cov.: 32 AF XY: 0.0858 AC XY: 6382 AN XY: 74414

African (AFR) AF: 0.122 AC: 5048 AN: 41522

American (AMR) AF: 0.0676 AC: 1033 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0398 AC: 192 AN: 4824

European-Finnish (FIN) AF: 0.0665 AC: 705 AN: 10598

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0834 AC: 5673 AN: 67996

Other (OTH) AF: 0.0671 AC: 142 AN: 2116

Alfa AF: 0.0856 Hom.: 1057

Bravo AF: 0.0884

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.53
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs10444517; hg19: chr12-94350823;