2-104887864-A-G

Variant names:

• chr2-104887864-A-G
• rs1026220
• ENST00000598623.1:n.345+34032A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000598623.1(ENSG00000269707):​n.345+34032A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,052 control chromosomes in the GnomAD database, including 28,816 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 0.61 (28816 hom., cov: 33)
• Consequence: ENSG00000269707 ENST00000598623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

Genes affected

ENSG00000269707 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 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
ENSG00000269707	ENST00000598623.1	n.345+34032A>G		intron_variant	Intron 2 of 2	5
ENSG00000269707	ENST00000653688.1	n.277-2488A>G		intron_variant	Intron 1 of 3
ENSG00000269707	ENST00000662784.1	n.167-2488A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93060 AN: 151934 Hom.: 28808 Cov.: 33

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.612 AC: 93111 AN: 152052 Hom.: 28816 Cov.: 33 AF XY: 0.614 AC XY: 45611 AN XY: 74324

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.633

Alfa AF: 0.606 Hom.: 37081

Bravo AF: 0.619

Asia WGS AF: 0.656 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	16
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1026220; hg19: chr2-105504322;