rs6557329

Variant names:

• chr6-153946959-A-G
• rs6557329

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 0.234 in 152,194 control chromosomes in the GnomAD database, including 4,534 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 0.23 (4534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35612 AN: 152078 Hom.: 4525 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.234 AC: 35628 AN: 152194 Hom.: 4534 Cov.: 32 AF XY: 0.243 AC XY: 18093 AN XY: 74400

African (AFR) AF: 0.165 AC: 6839 AN: 41552

American (AMR) AF: 0.397 AC: 6060 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 924 AN: 3466

East Asian (EAS) AF: 0.334 AC: 1727 AN: 5172

South Asian (SAS) AF: 0.392 AC: 1893 AN: 4830

European-Finnish (FIN) AF: 0.261 AC: 2769 AN: 10594

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14557 AN: 67998

Other (OTH) AF: 0.264 AC: 554 AN: 2102

Alfa AF: 0.248 Hom.: 2312

Bravo AF: 0.236

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		0.025

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6557329; hg19: chr6-154268094;