chr2-102264363-G-T

Variant names:

• chr2-102264363-G-T
• rs11123915
• ENST00000804381.1:n.240+1354G>T

Variant summary

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

The ENST00000804381.1(ENSG00000304533):​n.240+1354G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,992 control chromosomes in the GnomAD database, including 31,832 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 0.64 (31832 hom., cov: 32)
• Consequence: ENSG00000304533 ENST00000804381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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.240+1354G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97436 AN: 151874 Hom.: 31831 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.641 AC: 97469 AN: 151992 Hom.: 31832 Cov.: 32 AF XY: 0.648 AC XY: 48121 AN XY: 74294

African (AFR) AF: 0.576 AC: 23861 AN: 41424

American (AMR) AF: 0.554 AC: 8455 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2062 AN: 3472

East Asian (EAS) AF: 0.963 AC: 4989 AN: 5180

South Asian (SAS) AF: 0.744 AC: 3584 AN: 4820

European-Finnish (FIN) AF: 0.731 AC: 7703 AN: 10542

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44677 AN: 67966

Other (OTH) AF: 0.641 AC: 1356 AN: 2116

Alfa AF: 0.650 Hom.: 126456

Bravo AF: 0.620

Asia WGS AF: 0.828 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.76
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs11123915; hg19: chr2-102880823;