rs10046277

Variant names:

• chr6-32887304-C-T
• rs10046277

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 0.139 in 152,096 control chromosomes in the GnomAD database, including 1,739 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 0.14 (1739 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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: 0.139 AC: 21082 AN: 151978 Hom.: 1734 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.139 AC: 21124 AN: 152096 Hom.: 1739 Cov.: 32 AF XY: 0.139 AC XY: 10374 AN XY: 74374

African (AFR) AF: 0.222 AC: 9190 AN: 41460

American (AMR) AF: 0.100 AC: 1533 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3470

East Asian (EAS) AF: 0.0886 AC: 459 AN: 5180

South Asian (SAS) AF: 0.154 AC: 745 AN: 4822

European-Finnish (FIN) AF: 0.113 AC: 1201 AN: 10582

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6974 AN: 67976

Other (OTH) AF: 0.128 AC: 271 AN: 2112

Alfa AF: 0.117 Hom.: 1213

Bravo AF: 0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.16
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10046277; hg19: chr6-32855081;