chr6-32904224-A-G

Variant names:

• chr6-32904224-A-G
• rs2187688

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 0.525 in 151,944 control chromosomes in the GnomAD database, including 21,214 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 0.52 (21214 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 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: 0.525 AC: 79677 AN: 151826 Hom.: 21189 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.525 AC: 79752 AN: 151944 Hom.: 21214 Cov.: 31 AF XY: 0.524 AC XY: 38936 AN XY: 74264

African (AFR) AF: 0.575 AC: 23834 AN: 41416

American (AMR) AF: 0.472 AC: 7213 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1261 AN: 3468

East Asian (EAS) AF: 0.573 AC: 2964 AN: 5176

South Asian (SAS) AF: 0.532 AC: 2565 AN: 4818

European-Finnish (FIN) AF: 0.528 AC: 5559 AN: 10538

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34630 AN: 67942

Other (OTH) AF: 0.506 AC: 1067 AN: 2108

Alfa AF: 0.529 Hom.: 35605

Bravo AF: 0.521

Asia WGS AF: 0.567 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.11

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: rs2187688; hg19: chr6-32872001;