2-21357240-A-G

Position:

• chr2-21357240-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105374318 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374318	XR_939801.3	n.4449A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435237.1	n.120+135946A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000451476.1	n.246+36746A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000649482.1	n.474+393A>G		intron_variant, non_coding_transcript_variant
	ENST00000653699.1	n.517+393A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.327

Alfa AF: 0.310 Hom.: 7078

Bravo AF: 0.311

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs219562; hg19: chr2-21580112;