chr6-166174600-A-G

Variant names:

• chr6-166174600-A-G
• rs3099280

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 0.262 in 152,076 control chromosomes in the GnomAD database, including 5,469 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 0.26 (5469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 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: 0.262 AC: 39833 AN: 151958 Hom.: 5459 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.262 AC: 39881 AN: 152076 Hom.: 5469 Cov.: 32 AF XY: 0.266 AC XY: 19801 AN XY: 74338

African (AFR) AF: 0.299 AC: 12390 AN: 41468

American (AMR) AF: 0.195 AC: 2976 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2315 AN: 5168

South Asian (SAS) AF: 0.307 AC: 1483 AN: 4824

European-Finnish (FIN) AF: 0.305 AC: 3218 AN: 10566

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16206 AN: 67976

Other (OTH) AF: 0.234 AC: 493 AN: 2108

Alfa AF: 0.236 Hom.: 5793

Bravo AF: 0.255

Asia WGS AF: 0.334 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs3099280; hg19: chr6-166588088;