chr2-125311804-G-A

Variant names:

• chr2-125311804-G-A
• rs313289

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.604 AC: 25005 AN: 41430

American (AMR) AF: 0.228 AC: 3482 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3468

East Asian (EAS) AF: 0.0629 AC: 325 AN: 5168

South Asian (SAS) AF: 0.137 AC: 662 AN: 4818

European-Finnish (FIN) AF: 0.298 AC: 3148 AN: 10560

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20860 AN: 67980

Other (OTH) AF: 0.346 AC: 733 AN: 2116

Alfa AF: 0.312 Hom.: 4171

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
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs313289; hg19: chr2-126069381;