chr2-42894144-T-G

Variant names:

• chr2-42894144-T-G
• rs4953675
• ENST00000825116.1:n.838-39557T>G

Variant summary

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

The ENST00000825116.1(ENSG00000307331):​n.838-39557T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 151,994 control chromosomes in the GnomAD database, including 52,884 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 0.83 (52884 hom., cov: 29)
• Consequence: ENSG00000307331 ENST00000825116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

Genes affected

ENSG00000307331 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 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
ENSG00000307331	ENST00000825116.1	n.838-39557T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125851 AN: 151876 Hom.: 52811 Cov.: 29

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.829 AC: 125983 AN: 151994 Hom.: 52884 Cov.: 29 AF XY: 0.827 AC XY: 61420 AN XY: 74272

African (AFR) AF: 0.957 AC: 39681 AN: 41478

American (AMR) AF: 0.857 AC: 13090 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2893 AN: 3468

East Asian (EAS) AF: 0.654 AC: 3371 AN: 5154

South Asian (SAS) AF: 0.904 AC: 4321 AN: 4782

European-Finnish (FIN) AF: 0.737 AC: 7792 AN: 10574

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52244 AN: 67948

Other (OTH) AF: 0.830 AC: 1751 AN: 2110

Alfa AF: 0.788 Hom.: 23905

Bravo AF: 0.843

Asia WGS AF: 0.816 AC: 2837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-0.27

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Other links and lift over

dbSNP: rs4953675; hg19: chr2-43121284;