rs2235356

Variant names:

• chr22-50271920-G-A
• rs2235356
• ENST00000722692.1:n.16G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-50271920-G-A
• chr22-50271920-G-T

Variant summary

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

The ENST00000722692.1(ENSG00000294313):​n.16G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,604 control chromosomes in the GnomAD database, including 13,620 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 0.41 (13620 hom., cov: 30)
• Consequence: ENSG00000294313 ENST00000722692.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 10 publications found

Genes affected

ENSG00000294313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722692.1. 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
	ENSG00000294313	ENST00000722692.1		n.16G>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62719 AN: 151498 Hom.: 13618 Cov.: 30

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.414 AC: 62729 AN: 151604 Hom.: 13620 Cov.: 30 AF XY: 0.412 AC XY: 30546 AN XY: 74070

African (AFR) AF: 0.304 AC: 12560 AN: 41382

American (AMR) AF: 0.335 AC: 5111 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1391 AN: 3454

East Asian (EAS) AF: 0.586 AC: 2977 AN: 5084

South Asian (SAS) AF: 0.470 AC: 2257 AN: 4802

European-Finnish (FIN) AF: 0.433 AC: 4566 AN: 10556

Middle Eastern (MID) AF: 0.369 AC: 107 AN: 290

European-Non Finnish (NFE) AF: 0.477 AC: 32325 AN: 67758

Other (OTH) AF: 0.421 AC: 889 AN: 2110

Alfa AF: 0.445 Hom.: 15122

Bravo AF: 0.400

Asia WGS AF: 0.461 AC: 1589 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.5
DANN	Benign	0.89
PhyloP100		0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2235356; hg19: chr22-50710349;