2-210267691-A-G

Variant names:

• chr2-210267691-A-G
• rs1509569

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 0.412 in 152,050 control chromosomes in the GnomAD database, including 13,100 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 0.41 (13100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.771

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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: 0.412 AC: 62621 AN: 151932 Hom.: 13099 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.412 AC: 62621 AN: 152050 Hom.: 13100 Cov.: 32 AF XY: 0.410 AC XY: 30488 AN XY: 74310

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.397

Alfa AF: 0.430 Hom.: 29436

Bravo AF: 0.403

Asia WGS AF: 0.400 AC: 1388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1509569; hg19: chr2-211132415;