rs231727

Variant names:

• chr2-203876827-G-A
• rs231727

Your query was ambiguous. Multiple possible variants found:

• 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;