rs2430420

Variant names:

• chr2-10436100-G-A
• rs2430420
• ENST00000757451.1:n.251+3856G>A

Variant summary

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

The ENST00000757451.1(ENSG00000298698):​n.251+3856G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,132 control chromosomes in the GnomAD database, including 16,311 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 0.44 (16311 hom., cov: 33)
• Consequence: ENSG00000298698 ENST00000757451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74
• Publications: 5 publications found

Genes affected

ENSG00000298698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757451.1. 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
	ENSG00000298698	ENST00000757451.1		n.251+3856G>A		intron	N/A
	ENSG00000298698	ENST00000757452.1		n.132+3856G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66304 AN: 152014 Hom.: 16288 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.436 AC: 66370 AN: 152132 Hom.: 16311 Cov.: 33 AF XY: 0.436 AC XY: 32427 AN XY: 74370

African (AFR) AF: 0.672 AC: 27871 AN: 41502

American (AMR) AF: 0.312 AC: 4768 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2049 AN: 5150

South Asian (SAS) AF: 0.464 AC: 2238 AN: 4826

European-Finnish (FIN) AF: 0.413 AC: 4373 AN: 10598

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22819 AN: 67978

Other (OTH) AF: 0.392 AC: 828 AN: 2112

Alfa AF: 0.395 Hom.: 4514

Bravo AF: 0.433

Asia WGS AF: 0.447 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.48
PhyloP100		-2.7

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: rs2430420;

hg19: chr2-10576226;