rs219550

Positions:

• chr2-21316713-A-G
• chr2-21316713-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_939801.3(LOC105374318):​n.2593A>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 0.218 in 152,136 control chromosomes in the GnomAD database, including 4,685 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 (4685 hom., cov: 33)
• Consequence: LOC105374318 XR_939801.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

LOC105374318 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374318	XR_939801.3	n.2593A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435237.1	n.120+95419A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33139 AN: 152020 Hom.: 4658 Cov.: 33

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.218 AC: 33214 AN: 152136 Hom.: 4685 Cov.: 33 AF XY: 0.220 AC XY: 16361 AN XY: 74362

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.209

Alfa AF: 0.145 Hom.: 2635

Bravo AF: 0.235

Asia WGS AF: 0.269 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs219550; hg19: chr2-21539585;