3-21218878-G-T

Variant names:

• chr3-21218878-G-T
• rs10510511
• ENST00000634947.1:n.370+5810C>A

Variant summary

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

The ENST00000634947.1(ENSG00000282987):​n.370+5810C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0675 in 152,166 control chromosomes in the GnomAD database, including 1,223 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 0.067 (1223 hom., cov: 32)
• Consequence: ENSG00000282987 ENST00000634947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 5 publications found

Genes affected

ENSG00000282987 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376988	XR_940646.3	n.599-2356G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282987	ENST00000634947.1	n.370+5810C>A		intron_variant	Intron 2 of 2	5
ENSG00000294894	ENST00000726596.1	n.46+7827G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10252 AN: 152048 Hom.: 1217 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0302

Gnomad OTH AF: 0.0800

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

GnomAD4 genome AF: 0.0675 AC: 10266 AN: 152166 Hom.: 1223 Cov.: 32 AF XY: 0.0762 AC XY: 5667 AN XY: 74390

African (AFR) AF: 0.0116 AC: 483 AN: 41560

American (AMR) AF: 0.291 AC: 4447 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1240 AN: 5164

South Asian (SAS) AF: 0.205 AC: 985 AN: 4808

European-Finnish (FIN) AF: 0.0629 AC: 666 AN: 10594

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0302 AC: 2051 AN: 67996

Other (OTH) AF: 0.0806 AC: 170 AN: 2110

Alfa AF: 0.0504 Hom.: 1141

Bravo AF: 0.0813

Asia WGS AF: 0.229 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.47
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs10510511; hg19: chr3-21260370;