chr6-32783837-G-C

Variant names:

• chr6-32783837-G-C
• rs17429127

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 0.0585 in 152,154 control chromosomes in the GnomAD database, including 339 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 0.059 (339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0887 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0586 AC: 8907 AN: 152036 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0585 AC: 8902 AN: 152154 Hom.: 339 Cov.: 32 AF XY: 0.0602 AC XY: 4475 AN XY: 74386

African (AFR) AF: 0.0169 AC: 702 AN: 41526

American (AMR) AF: 0.0781 AC: 1193 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3470

East Asian (EAS) AF: 0.0232 AC: 120 AN: 5182

South Asian (SAS) AF: 0.0959 AC: 463 AN: 4826

European-Finnish (FIN) AF: 0.0889 AC: 941 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0725 AC: 4931 AN: 67978

Other (OTH) AF: 0.0729 AC: 154 AN: 2112

Alfa AF: 0.0264 Hom.: 18

Bravo AF: 0.0533

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.77
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17429127; hg19: chr6-32751614;