rs313289

Positions:

• chr2-125311804-G-A

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 0.365 in 152,040 control chromosomes in the GnomAD database, including 12,045 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 0.36 (12045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55359 AN: 151922 Hom.: 12015 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.365 AC: 55429 AN: 152040 Hom.: 12045 Cov.: 32 AF XY: 0.356 AC XY: 26479 AN XY: 74306

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.0629

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.346

Alfa AF: 0.312 Hom.: 3784

Bravo AF: 0.370

Asia WGS AF: 0.128 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs313289; hg19: chr2-126069381;