rs2794521

Variant names:

• chr1-159715306-C-T
• rs2794521
• ENST00000751816.1:n.108-11221C>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-11221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 149,672 control chromosomes in the GnomAD database, including 45,152 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 0.77 (45152 hom., cov: 23)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 138 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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
	ENSG00000297913	ENST00000751816.1		n.108-11221C>T		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-11221C>T		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-11221C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.775 AC: 115874 AN: 149554 Hom.: 45101 Cov.: 23

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.775 AC: 115985 AN: 149672 Hom.: 45152 Cov.: 23 AF XY: 0.777 AC XY: 56704 AN XY: 72934

African (AFR) AF: 0.855 AC: 34773 AN: 40690

American (AMR) AF: 0.802 AC: 12033 AN: 15006

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2863 AN: 3452

East Asian (EAS) AF: 0.820 AC: 4128 AN: 5036

South Asian (SAS) AF: 0.671 AC: 3136 AN: 4674

European-Finnish (FIN) AF: 0.803 AC: 8112 AN: 10102

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48531 AN: 67446

Other (OTH) AF: 0.780 AC: 1617 AN: 2072

Alfa AF: 0.745 Hom.: 50576

Bravo AF: 0.779

Asia WGS AF: 0.739 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		-2.2

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: rs2794521;

hg19: chr1-159685096;