chr2-180151406-A-G

Variant names:

• chr2-180151406-A-G
• rs17180327

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 0.252 in 152,092 control chromosomes in the GnomAD database, including 6,149 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 0.25 (6149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 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: 0.253 AC: 38383 AN: 151974 Hom.: 6155 Cov.: 32

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.252 AC: 38356 AN: 152092 Hom.: 6149 Cov.: 32 AF XY: 0.250 AC XY: 18581 AN XY: 74330

African (AFR) AF: 0.0667 AC: 2770 AN: 41550

American (AMR) AF: 0.247 AC: 3773 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1168 AN: 5168

South Asian (SAS) AF: 0.155 AC: 749 AN: 4826

European-Finnish (FIN) AF: 0.335 AC: 3540 AN: 10554

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24185 AN: 67934

Other (OTH) AF: 0.274 AC: 578 AN: 2110

Alfa AF: 0.316 Hom.: 27127

Bravo AF: 0.237

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs17180327; hg19: chr2-181016133;