rs10482872

chr21-15558677-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634644.1(ENSG00000229425):n.354+16593C>G variant causes a intron, non coding transcript 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: ENST00000634644.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369302	XR_001754972.2	n.356+16593C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634644.1	n.354+16593C>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.00506

Gnomad4 OTH AF: 0.102

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.3
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10482872; hg19: chr21-16930996;