6-103335483-T-C

Variant names:

• chr6-103335483-T-C
• rs2399927

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 0.865 in 152,096 control chromosomes in the GnomAD database, including 56,973 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 0.87 (56973 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.865 AC: 131515 AN: 151978 Hom.: 56945 Cov.: 30

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.865 AC: 131595 AN: 152096 Hom.: 56973 Cov.: 30 AF XY: 0.866 AC XY: 64390 AN XY: 74330

African (AFR) AF: 0.849 AC: 35217 AN: 41500

American (AMR) AF: 0.866 AC: 13233 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2973 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4649 AN: 5154

South Asian (SAS) AF: 0.891 AC: 4286 AN: 4812

European-Finnish (FIN) AF: 0.897 AC: 9497 AN: 10582

Middle Eastern (MID) AF: 0.880 AC: 257 AN: 292

European-Non Finnish (NFE) AF: 0.866 AC: 58894 AN: 67984

Other (OTH) AF: 0.868 AC: 1833 AN: 2112

Alfa AF: 0.863 Hom.: 53577

Bravo AF: 0.859

Asia WGS AF: 0.886 AC: 3079 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	0.21
DANN	Benign	0.15
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2399927; hg19: chr6-103783358;