rs2352714

Variant names:

• chr2-7350025-A-G
• rs2352714
• ENST00000812800.1:n.312+55892A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-7350025-A-G
• chr2-7350025-A-T

Variant summary

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

The ENST00000812800.1(ENSG00000229727):​n.312+55892A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,108 control chromosomes in the GnomAD database, including 5,922 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 0.25 (5922 hom., cov: 32)
• Consequence: ENSG00000229727 ENST00000812800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 0 publications found

Genes affected

ENSG00000229727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812800.1. 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
	ENSG00000229727	ENST00000812800.1		n.312+55892A>G		intron	N/A
	ENSG00000229727	ENST00000812801.1		n.447-22104A>G		intron	N/A
	ENSG00000229727	ENST00000812802.1		n.447-22104A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38543 AN: 151990 Hom.: 5917 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.254 AC: 38573 AN: 152108 Hom.: 5922 Cov.: 32 AF XY: 0.258 AC XY: 19202 AN XY: 74340

African (AFR) AF: 0.319 AC: 13227 AN: 41476

American (AMR) AF: 0.322 AC: 4926 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3472

East Asian (EAS) AF: 0.735 AC: 3786 AN: 5154

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4808

European-Finnish (FIN) AF: 0.195 AC: 2062 AN: 10590

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11879 AN: 68002

Other (OTH) AF: 0.273 AC: 577 AN: 2110

Alfa AF: 0.209 Hom.: 499

Bravo AF: 0.271

Asia WGS AF: 0.476 AC: 1655 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	0.26
DANN	Benign	0.18
PhyloP100		-0.69

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: rs2352714;

hg19: chr2-7490156;