chr2-156896859-A-T

Variant names:

• chr2-156896859-A-T
• rs295796
• ENST00000762467.1:n.194+10297A>T

Variant summary

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

The ENST00000762467.1(ENSG00000287048):​n.194+10297A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 151,636 control chromosomes in the GnomAD database, including 44,390 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 0.74 (44390 hom., cov: 32)
• Consequence: ENSG00000287048 ENST00000762467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 3 publications found

Genes affected

ENSG00000287048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 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
ENSG00000287048	ENST00000762467.1	n.194+10297A>T		intron_variant	Intron 2 of 2
ENSG00000287048	ENST00000762468.1	n.242+10297A>T		intron_variant	Intron 3 of 3
ENSG00000287048	ENST00000762469.1	n.362+10297A>T		intron_variant	Intron 4 of 4
ENSG00000287048	ENST00000762470.1	n.263+10297A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112561 AN: 151518 Hom.: 44366 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.743 AC: 112627 AN: 151636 Hom.: 44390 Cov.: 32 AF XY: 0.743 AC XY: 55028 AN XY: 74066

African (AFR) AF: 0.455 AC: 18822 AN: 41402

American (AMR) AF: 0.765 AC: 11626 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3044 AN: 3460

East Asian (EAS) AF: 0.843 AC: 4291 AN: 5090

South Asian (SAS) AF: 0.807 AC: 3897 AN: 4830

European-Finnish (FIN) AF: 0.835 AC: 8854 AN: 10606

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59484 AN: 67750

Other (OTH) AF: 0.749 AC: 1575 AN: 2102

Alfa AF: 0.768 Hom.: 3022

Bravo AF: 0.726

Asia WGS AF: 0.785 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.10
DANN	Benign	0.40
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs295796; hg19: chr2-157753371;