2-170155605-A-G

Variant names:

• chr2-170155605-A-G
• rs16857804

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 0.299 in 151,954 control chromosomes in the GnomAD database, including 7,303 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 0.30 (7303 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 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: 0.299 AC: 45390 AN: 151836 Hom.: 7304 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.299 AC: 45405 AN: 151954 Hom.: 7303 Cov.: 32 AF XY: 0.306 AC XY: 22692 AN XY: 74278

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.314

Alfa AF: 0.302 Hom.: 9300

Bravo AF: 0.291

Asia WGS AF: 0.499 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16857804; hg19: chr2-171012115;