rs1072038

Positions:

• chr2-180485103-A-G

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 0.116 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.0793

Gnomad4 ASJ AF: 0.0926

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0834

Gnomad4 NFE AF: 0.0700

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0853 Hom.: 125

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1072038; hg19: chr2-181349830;