rs10829848

Variant names:

• chr10-130949624-C-T
• rs10829848
• ENST00000769416.1:n.495-18536C>T

Variant summary

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

The ENST00000769416.1(ENSG00000300141):​n.495-18536C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,176 control chromosomes in the GnomAD database, including 1,978 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 0.15 (1978 hom., cov: 33)
• Consequence: ENSG00000300141 ENST00000769416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 9 publications found

Genes affected

ENSG00000300141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000769416.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300141	ENST00000769416.1		n.495-18536C>T		intron	N/A
	ENSG00000300141	ENST00000769417.1		n.446-11921C>T		intron	N/A
	ENSG00000300141	ENST00000769418.1		n.869-11921C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22931 AN: 152056 Hom.: 1981 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.151 AC: 22937 AN: 152176 Hom.: 1978 Cov.: 33 AF XY: 0.153 AC XY: 11353 AN XY: 74384

African (AFR) AF: 0.123 AC: 5091 AN: 41552

American (AMR) AF: 0.122 AC: 1868 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2009 AN: 5130

South Asian (SAS) AF: 0.152 AC: 734 AN: 4818

European-Finnish (FIN) AF: 0.197 AC: 2084 AN: 10598

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10208 AN: 68002

Other (OTH) AF: 0.143 AC: 303 AN: 2112

Alfa AF: 0.152 Hom.: 5295

Bravo AF: 0.145

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.52
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10829848; hg19: chr10-132747887;