rs231727

Positions:

• chr2-203876827-G-A
• chr2-203876827-G-C

Variant summary

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

The variant allele was found at a frequency of 0.378 in 151,868 control chromosomes in the GnomAD database, including 11,292 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 0.38 (11292 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.203876827G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57351 AN: 151750 Hom.: 11280 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.378 AC: 57408 AN: 151868 Hom.: 11292 Cov.: 31 AF XY: 0.385 AC XY: 28556 AN XY: 74204

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.329

Alfa AF: 0.339 Hom.: 2876

Bravo AF: 0.377

Asia WGS AF: 0.392 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs231727; hg19: chr2-204741550;