chr2-21357240-A-G

Variant names:

• chr2-21357240-A-G
• rs219562
• XR_939801.3:n.4449A>G

Variant summary

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

The XR_939801.3(LOC105374318):​n.4449A>G 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 0.309 in 152,098 control chromosomes in the GnomAD database, including 7,426 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 0.31 (7426 hom., cov: 33)
• Consequence: LOC105374318 XR_939801.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 3 publications found

Genes affected

LOC105374318 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435237.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231204	ENST00000435237.1	TSL:3	n.120+135946A>G		intron	N/A
	ENSG00000231204	ENST00000451476.1	TSL:5	n.246+36746A>G		intron	N/A
	ENSG00000231204	ENST00000649482.1		n.474+393A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 47021 AN: 151978 Hom.: 7430 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.309 AC: 47047 AN: 152098 Hom.: 7426 Cov.: 33 AF XY: 0.307 AC XY: 22838 AN XY: 74354

African (AFR) AF: 0.317 AC: 13129 AN: 41468

American (AMR) AF: 0.271 AC: 4144 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1291 AN: 5176

South Asian (SAS) AF: 0.351 AC: 1691 AN: 4820

European-Finnish (FIN) AF: 0.267 AC: 2822 AN: 10580

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.315 AC: 21410 AN: 67982

Other (OTH) AF: 0.327 AC: 690 AN: 2112

Alfa AF: 0.311 Hom.: 19314

Bravo AF: 0.311

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.27
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs219562; hg19: chr2-21580112;