chr2-103526090-T-G

Variant names:

• chr2-103526090-T-G
• rs1022298
• ENST00000835671.1:n.261+24780T>G

Variant summary

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

The ENST00000835671.1(ENSG00000308676):​n.261+24780T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,042 control chromosomes in the GnomAD database, including 18,583 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 0.48 (18583 hom., cov: 32)
• Consequence: ENSG00000308676 ENST00000835671.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 6 publications found

Genes affected

ENSG00000308676 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 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
ENSG00000308676	ENST00000835671.1	n.261+24780T>G		intron_variant	Intron 3 of 4
ENSG00000308676	ENST00000835672.1	n.211+24780T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72655 AN: 151920 Hom.: 18559 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.478 AC: 72720 AN: 152042 Hom.: 18583 Cov.: 32 AF XY: 0.471 AC XY: 35030 AN XY: 74318

African (AFR) AF: 0.622 AC: 25807 AN: 41470

American (AMR) AF: 0.385 AC: 5879 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3468

East Asian (EAS) AF: 0.0195 AC: 101 AN: 5178

South Asian (SAS) AF: 0.241 AC: 1160 AN: 4818

European-Finnish (FIN) AF: 0.471 AC: 4973 AN: 10566

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.468 AC: 31774 AN: 67948

Other (OTH) AF: 0.477 AC: 1008 AN: 2114

Alfa AF: 0.460 Hom.: 69892

Bravo AF: 0.477

Asia WGS AF: 0.166 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.0
DANN	Benign	0.79
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs1022298; hg19: chr2-104142548;