6-50643622-T-A

Variant names:

• chr6-50643622-T-A
• rs280306

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 0.177 in 151,886 control chromosomes in the GnomAD database, including 3,804 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 (3804 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26775 AN: 151768 Hom.: 3789 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.177 AC: 26826 AN: 151886 Hom.: 3804 Cov.: 31 AF XY: 0.173 AC XY: 12834 AN XY: 74258

African (AFR) AF: 0.403 AC: 16663 AN: 41334

American (AMR) AF: 0.113 AC: 1731 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3468

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5174

South Asian (SAS) AF: 0.123 AC: 590 AN: 4810

European-Finnish (FIN) AF: 0.0578 AC: 611 AN: 10566

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0903 AC: 6139 AN: 67956

Other (OTH) AF: 0.156 AC: 328 AN: 2104

Alfa AF: 0.142 Hom.: 320

Bravo AF: 0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.18
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs280306; hg19: chr6-50611335;