rs540006

Variant names:

• chr2-70556290-T-C
• rs540006
• ENST00000726429.1:n.741+2898T>C

Variant summary

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

The ENST00000726429.1(ENSG00000294870):​n.741+2898T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.058 in 149,082 control chromosomes in the GnomAD database, including 331 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 0.058 (331 hom., cov: 30)
• Consequence: ENSG00000294870 ENST00000726429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 1 publications found

Genes affected

ENSG00000294870 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726429.1. 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
	ENSG00000294870	ENST00000726429.1		n.741+2898T>C		intron	N/A
	ENSG00000294870	ENST00000726430.1		n.726+2890T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0581 AC: 8657 AN: 148984 Hom.: 329 Cov.: 30

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0777

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0632

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0580 AC: 8653 AN: 149082 Hom.: 331 Cov.: 30 AF XY: 0.0592 AC XY: 4294 AN XY: 72568

African (AFR) AF: 0.0172 AC: 700 AN: 40680

American (AMR) AF: 0.0839 AC: 1266 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.0777 AC: 267 AN: 3436

East Asian (EAS) AF: 0.148 AC: 755 AN: 5114

South Asian (SAS) AF: 0.120 AC: 572 AN: 4784

European-Finnish (FIN) AF: 0.0712 AC: 656 AN: 9210

Middle Eastern (MID) AF: 0.0552 AC: 16 AN: 290

European-Non Finnish (NFE) AF: 0.0632 AC: 4265 AN: 67496

Other (OTH) AF: 0.0753 AC: 156 AN: 2072

Alfa AF: 0.0634 Hom.: 445

Bravo AF: 0.0582

Asia WGS AF: 0.141 AC: 486 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		0.071

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: rs540006;

hg19: chr2-70783422;