rs1356702

Variant names:

• chr2-221640484-A-G
• rs1356702
• ENST00000453706.2:n.56-1124A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-221640484-A-G
• chr2-221640484-A-T

Variant summary

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

The ENST00000658881.1(ENSG00000234446):​n.115-1124A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,100 control chromosomes in the GnomAD database, including 3,843 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 0.22 (3843 hom., cov: 32)
• Consequence: ENSG00000234446 ENST00000658881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 0 publications found

Genes affected

ENSG00000234446 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658881.1. 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
	ENSG00000234446	ENST00000453706.2	TSL:5	n.56-1124A>G		intron	N/A
	ENSG00000234446	ENST00000658881.1		n.115-1124A>G		intron	N/A
	ENSG00000234446	ENST00000664786.1		n.61-1124A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33333 AN: 151982 Hom.: 3833 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.219 AC: 33385 AN: 152100 Hom.: 3843 Cov.: 32 AF XY: 0.224 AC XY: 16657 AN XY: 74370

African (AFR) AF: 0.246 AC: 10193 AN: 41466

American (AMR) AF: 0.243 AC: 3715 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1902 AN: 5168

South Asian (SAS) AF: 0.232 AC: 1117 AN: 4818

European-Finnish (FIN) AF: 0.211 AC: 2234 AN: 10576

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12563 AN: 67988

Other (OTH) AF: 0.248 AC: 525 AN: 2114

Alfa AF: 0.205 Hom.: 391

Bravo AF: 0.223

Asia WGS AF: 0.296 AC: 1026 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.79
PhyloP100		0.33

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: rs1356702;

hg19: chr2-222505204;