rs79480871

Variant names:

• chr2-24471603-C-T
• rs79480871
• ENST00000826690.1:n.447-4195C>T

Variant summary

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

The ENST00000826690.1(ENSG00000286829):​n.447-4195C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.094 in 152,190 control chromosomes in the GnomAD database, including 782 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 0.094 (782 hom., cov: 32)
• Consequence: ENSG00000286829 ENST00000826690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.718
• Publications: 17 publications found

Genes affected

ENSG00000286829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826690.1. 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
	ENSG00000286829	ENST00000826690.1		n.447-4195C>T		intron	N/A
	ENSG00000286829	ENST00000826691.1		n.468-1410C>T		intron	N/A
	ENSG00000286829	ENST00000826692.1		n.255-1410C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14286 AN: 152072 Hom.: 783 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.0999

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0660

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.0940 AC: 14301 AN: 152190 Hom.: 782 Cov.: 32 AF XY: 0.0953 AC XY: 7092 AN XY: 74386

African (AFR) AF: 0.145 AC: 6029 AN: 41494

American (AMR) AF: 0.0921 AC: 1409 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.0992 AC: 514 AN: 5184

South Asian (SAS) AF: 0.115 AC: 552 AN: 4816

European-Finnish (FIN) AF: 0.0660 AC: 698 AN: 10582

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0663 AC: 4511 AN: 68022

Other (OTH) AF: 0.0964 AC: 204 AN: 2116

Alfa AF: 0.0774 Hom.: 1083

Bravo AF: 0.0983

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.5
DANN	Benign	0.79
PhyloP100		0.72

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs79480871;

hg19: chr2-24694472;