chr2-102298194-A-G

Variant names:

• chr2-102298194-A-G
• rs10515922
• ENST00000804381.1:n.513-239A>G

Variant summary

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

The ENST00000804381.1(ENSG00000304533):​n.513-239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 152,156 control chromosomes in the GnomAD database, including 509 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 0.070 (509 hom., cov: 32)
• Consequence: ENSG00000304533 ENST00000804381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 10 publications found

Genes affected

ENSG00000304533 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 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
ENSG00000304533	ENST00000804381.1	n.513-239A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10673 AN: 152038 Hom.: 509 Cov.: 32

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0932

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0701 AC: 10670 AN: 152156 Hom.: 509 Cov.: 32 AF XY: 0.0712 AC XY: 5294 AN XY: 74394

African (AFR) AF: 0.0205 AC: 850 AN: 41518

American (AMR) AF: 0.0609 AC: 932 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3470

East Asian (EAS) AF: 0.156 AC: 805 AN: 5158

South Asian (SAS) AF: 0.0665 AC: 321 AN: 4830

European-Finnish (FIN) AF: 0.101 AC: 1070 AN: 10588

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0932 AC: 6333 AN: 67972

Other (OTH) AF: 0.0577 AC: 122 AN: 2116

Alfa AF: 0.0810 Hom.: 889

Bravo AF: 0.0630

Asia WGS AF: 0.0910 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.49
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10515922; hg19: chr2-102914654;