rs522447

Variant names:

• chr6-103164784-C-T
• rs522447

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 0.891 in 152,232 control chromosomes in the GnomAD database, including 60,561 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 0.89 (60561 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.936 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: 0.891 AC: 135550 AN: 152114 Hom.: 60508 Cov.: 33

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.891 AC: 135658 AN: 152232 Hom.: 60561 Cov.: 33 AF XY: 0.894 AC XY: 66534 AN XY: 74422

African (AFR) AF: 0.852 AC: 35380 AN: 41520

American (AMR) AF: 0.905 AC: 13840 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3002 AN: 3472

East Asian (EAS) AF: 0.802 AC: 4136 AN: 5154

South Asian (SAS) AF: 0.959 AC: 4635 AN: 4834

European-Finnish (FIN) AF: 0.945 AC: 10031 AN: 10616

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61740 AN: 68022

Other (OTH) AF: 0.882 AC: 1864 AN: 2114

Alfa AF: 0.901 Hom.: 111841

Bravo AF: 0.883

Asia WGS AF: 0.889 AC: 3094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.6
DANN	Benign	0.53
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs522447; hg19: chr6-103612659;