chr6-170280901-G-A

Variant names:

• chr6-170280901-G-A
• rs2180052

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 0.183 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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.133 AC: 5540 AN: 41564

American (AMR) AF: 0.176 AC: 2688 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3470

East Asian (EAS) AF: 0.862 AC: 4456 AN: 5172

South Asian (SAS) AF: 0.387 AC: 1870 AN: 4828

European-Finnish (FIN) AF: 0.184 AC: 1954 AN: 10602

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10200 AN: 68030

Other (OTH) AF: 0.179 AC: 379 AN: 2116

Alfa AF: 0.159 Hom.: 4907

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2180052; hg19: chr6-170589989;