ENST00000670545.1:n.110-8524A>T

Variant names:

• chr2-156877938-A-T
• rs295826
• ENST00000670545.1:n.110-8524A>T

Variant summary

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

The ENST00000670545.1(ENSG00000287048):​n.110-8524A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 151,982 control chromosomes in the GnomAD database, including 43,871 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 0.73 (43871 hom., cov: 32)
• Consequence: ENSG00000287048 ENST00000670545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670545.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287048	ENST00000670545.1		n.110-8524A>T		intron	N/A
	ENSG00000287048	ENST00000762467.1		n.94-8524A>T		intron	N/A
	ENSG00000287048	ENST00000762468.1		n.142-8524A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111113 AN: 151864 Hom.: 43850 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.731 AC: 111166 AN: 151982 Hom.: 43871 Cov.: 32 AF XY: 0.732 AC XY: 54341 AN XY: 74262

African (AFR) AF: 0.409 AC: 16956 AN: 41446

American (AMR) AF: 0.758 AC: 11548 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3054 AN: 3472

East Asian (EAS) AF: 0.841 AC: 4332 AN: 5148

South Asian (SAS) AF: 0.807 AC: 3887 AN: 4816

European-Finnish (FIN) AF: 0.835 AC: 8837 AN: 10584

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59958 AN: 67972

Other (OTH) AF: 0.740 AC: 1561 AN: 2110

Alfa AF: 0.801 Hom.: 6049

Bravo AF: 0.711

Asia WGS AF: 0.784 AC: 2712 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.15
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs295826; hg19: chr2-157734450;