rs2102010

Variant names:

• chr4-53877079-A-G
• rs2102010
• ENST00000507166.5:c.1018-397846A>G

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1018-397846A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,030 control chromosomes in the GnomAD database, including 38,674 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 0.69 (38674 hom., cov: 33)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282278	ENST00000507166.5	c.1018-397846A>G		intron_variant	Intron 12 of 23	2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104902 AN: 151912 Hom.: 38654 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.690 AC: 104965 AN: 152030 Hom.: 38674 Cov.: 33 AF XY: 0.699 AC XY: 51958 AN XY: 74346

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.958

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.714

Alfa AF: 0.733 Hom.: 5346

Bravo AF: 0.674

Asia WGS AF: 0.878 AC: 3051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2102010; hg19: chr4-54743246;