rs10482872

Variant names:

• chr21-15558677-G-C
• rs10482872
• ENST00000634644.1:n.354+16593C>G

Variant summary

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

The ENST00000653886.1(ENSG00000229425):​n.330+16593C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,140 control chromosomes in the GnomAD database, including 2,793 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 0.12 (2793 hom., cov: 33)
• Consequence: ENSG00000229425 ENST00000653886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 0 publications found

Genes affected

ENSG00000229425 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653886.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229425	ENST00000634644.1	TSL:5	n.354+16593C>G		intron	N/A
	ENSG00000229425	ENST00000634708.1	TSL:5	n.354+16593C>G		intron	N/A
	ENSG00000229425	ENST00000635525.2	TSL:5	n.402+16593C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18008 AN: 152022 Hom.: 2778 Cov.: 33

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.00506

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.119 AC: 18062 AN: 152140 Hom.: 2793 Cov.: 33 AF XY: 0.119 AC XY: 8854 AN XY: 74396

African (AFR) AF: 0.347 AC: 14369 AN: 41462

American (AMR) AF: 0.131 AC: 2004 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3472

East Asian (EAS) AF: 0.157 AC: 814 AN: 5180

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4830

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.00506 AC: 344 AN: 67990

Other (OTH) AF: 0.102 AC: 215 AN: 2116

Alfa AF: 0.0679 Hom.: 183

Bravo AF: 0.138

Asia WGS AF: 0.0850 AC: 299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10482872;

hg19: chr21-16930996;