rs10105219

Variant names:

• chr8-82944940-T-C
• rs10105219
• ENST00000522123.1:n.57+13700A>G

Variant summary

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

The ENST00000522123.1(ENSG00000253836):​n.57+13700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,762 control chromosomes in the GnomAD database, including 20,264 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 0.50 (20264 hom., cov: 33)
• Consequence: ENSG00000253836 ENST00000522123.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 2 publications found

Genes affected

ENSG00000253836 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522123.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927141	NR_134295.1		n.361-16256T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253836	ENST00000522123.1	TSL:3	n.57+13700A>G		intron	N/A
	ENSG00000254394	ENST00000524359.1	TSL:3	n.361-16256T>C		intron	N/A
	ENSG00000254394	ENST00000663058.1		n.1029-7397T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76047 AN: 151644 Hom.: 20225 Cov.: 33

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.502 AC: 76135 AN: 151762 Hom.: 20264 Cov.: 33 AF XY: 0.496 AC XY: 36820 AN XY: 74164

African (AFR) AF: 0.690 AC: 28593 AN: 41464

American (AMR) AF: 0.420 AC: 6408 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1844 AN: 3462

East Asian (EAS) AF: 0.185 AC: 955 AN: 5172

South Asian (SAS) AF: 0.405 AC: 1953 AN: 4822

European-Finnish (FIN) AF: 0.406 AC: 4281 AN: 10546

Middle Eastern (MID) AF: 0.469 AC: 136 AN: 290

European-Non Finnish (NFE) AF: 0.450 AC: 30510 AN: 67752

Other (OTH) AF: 0.507 AC: 1066 AN: 2104

Alfa AF: 0.490 Hom.: 21349

Bravo AF: 0.509

Asia WGS AF: 0.338 AC: 1168 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.61
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10105219; hg19: chr8-83857175;