chr2-117516426-T-C

Variant names:

• chr2-117516426-T-C
• rs4849561
• ENST00000752778.1:n.463-14872A>G

Variant summary

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

The ENST00000752778.1(ENSG00000298065):​n.463-14872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,094 control chromosomes in the GnomAD database, including 55,156 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 0.85 (55156 hom., cov: 32)
• Consequence: ENSG00000298065 ENST00000752778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 4 publications found

Genes affected

ENSG00000298065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752778.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298065	ENST00000752778.1		n.463-14872A>G		intron	N/A
	ENSG00000298065	ENST00000752779.1		n.536-14872A>G		intron	N/A
	ENSG00000298065	ENST00000752780.1		n.378-14872A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129167 AN: 151976 Hom.: 55107 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.850 AC: 129271 AN: 152094 Hom.: 55156 Cov.: 32 AF XY: 0.851 AC XY: 63287 AN XY: 74360

African (AFR) AF: 0.795 AC: 32987 AN: 41472

American (AMR) AF: 0.893 AC: 13651 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3144 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5168 AN: 5172

South Asian (SAS) AF: 0.930 AC: 4472 AN: 4808

European-Finnish (FIN) AF: 0.851 AC: 9003 AN: 10574

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58172 AN: 67986

Other (OTH) AF: 0.860 AC: 1815 AN: 2110

Alfa AF: 0.858 Hom.: 94514

Bravo AF: 0.850

Asia WGS AF: 0.954 AC: 3313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.76
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs4849561; hg19: chr2-118274002;