2-180485103-A-G

Variant names:

• chr2-180485103-A-G
• rs1072038

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 0.116 in 152,022 control chromosomes in the GnomAD database, including 1,309 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 0.12 (1309 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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: 0.116 AC: 17623 AN: 151902 Hom.: 1304 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0793

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0834

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.116 AC: 17637 AN: 152022 Hom.: 1309 Cov.: 31 AF XY: 0.119 AC XY: 8806 AN XY: 74302

African (AFR) AF: 0.202 AC: 8387 AN: 41450

American (AMR) AF: 0.0793 AC: 1210 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0926 AC: 321 AN: 3468

East Asian (EAS) AF: 0.169 AC: 867 AN: 5140

South Asian (SAS) AF: 0.174 AC: 835 AN: 4810

European-Finnish (FIN) AF: 0.0834 AC: 884 AN: 10602

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0700 AC: 4759 AN: 67976

Other (OTH) AF: 0.122 AC: 257 AN: 2112

Alfa AF: 0.0889 Hom.: 141

Bravo AF: 0.118

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.83
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1072038; hg19: chr2-181349830;