rs214034

Variant names:

• chr2-17807391-A-C
• rs214034
• ENST00000750479.1:n.454-2437T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-17807391-A-C
• chr2-17807391-A-T

Variant summary

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

The ENST00000750479.1(ENSG00000297720):​n.454-2437T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,894 control chromosomes in the GnomAD database, including 38,134 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 0.70 (38134 hom., cov: 30)
• Consequence: ENSG00000297720 ENST00000750479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774
• Publications: 4 publications found

Genes affected

ENSG00000297720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750479.1. 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
	ENSG00000297720	ENST00000750479.1		n.454-2437T>G		intron	N/A
	ENSG00000297720	ENST00000750480.1		n.636+1122T>G		intron	N/A
	ENSG00000297720	ENST00000750481.1		n.596-2437T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106589 AN: 151776 Hom.: 38091 Cov.: 30

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.702 AC: 106692 AN: 151894 Hom.: 38134 Cov.: 30 AF XY: 0.706 AC XY: 52421 AN XY: 74200

African (AFR) AF: 0.762 AC: 31554 AN: 41402

American (AMR) AF: 0.766 AC: 11696 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2384 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5100 AN: 5174

South Asian (SAS) AF: 0.891 AC: 4289 AN: 4816

European-Finnish (FIN) AF: 0.588 AC: 6191 AN: 10532

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43182 AN: 67924

Other (OTH) AF: 0.694 AC: 1463 AN: 2108

Alfa AF: 0.497 Hom.: 944

Bravo AF: 0.716

Asia WGS AF: 0.915 AC: 3176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.26
PhyloP100		-0.77

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: rs214034;

hg19: chr2-17988658;