chr2-72886395-G-A

Variant names:

• chr2-72886395-G-A
• rs2421095
• ENST00000840248.1:n.165-680C>T

Variant summary

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

The ENST00000840248.1(ENSG00000309317):​n.165-680C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,230 control chromosomes in the GnomAD database, including 57,068 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 0.86 (57068 hom., cov: 33)
• Consequence: ENSG00000309317 ENST00000840248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 10 publications found

Genes affected

ENSG00000309317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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
ENSG00000309317	ENST00000840248.1	n.165-680C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.861 AC: 131005 AN: 152112 Hom.: 57046 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.861 AC: 131070 AN: 152230 Hom.: 57068 Cov.: 33 AF XY: 0.866 AC XY: 64430 AN XY: 74428

African (AFR) AF: 0.724 AC: 30049 AN: 41504

American (AMR) AF: 0.905 AC: 13849 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3246 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5143 AN: 5182

South Asian (SAS) AF: 0.935 AC: 4513 AN: 4826

European-Finnish (FIN) AF: 0.947 AC: 10051 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61332 AN: 68020

Other (OTH) AF: 0.869 AC: 1834 AN: 2110

Alfa AF: 0.890 Hom.: 99319

Bravo AF: 0.849

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.23
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2421095; hg19: chr2-73113524;