rs2180052

chr6-170280901-G-Achr6-170280901-G-C

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 0.183 in 152,284 control chromosomes in the GnomAD database, including 3,968 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 0.18 (3968 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27785 AN: 152166 Hom.: 3969 Cov.: 34

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.183 AC: 27809 AN: 152284 Hom.: 3968 Cov.: 34 AF XY: 0.191 AC XY: 14200 AN XY: 74450

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.179

Alfa AF: 0.152 Hom.: 2758

Bravo AF: 0.181

Asia WGS AF: 0.611 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.65
Dann	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2180052; hg19: chr6-170589989;