10-67883584-T-C

Variant names:

• chr10-67883584-T-C
• rs3758391

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 0.627 in 151,930 control chromosomes in the GnomAD database, including 30,703 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 0.63 (30703 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 98 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 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: 0.627 AC: 95172 AN: 151812 Hom.: 30682 Cov.: 30

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.627 AC: 95233 AN: 151930 Hom.: 30703 Cov.: 30 AF XY: 0.618 AC XY: 45844 AN XY: 74234

African (AFR) AF: 0.649 AC: 26894 AN: 41450

American (AMR) AF: 0.570 AC: 8680 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2375 AN: 3468

East Asian (EAS) AF: 0.151 AC: 780 AN: 5152

South Asian (SAS) AF: 0.455 AC: 2192 AN: 4814

European-Finnish (FIN) AF: 0.590 AC: 6224 AN: 10544

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46098 AN: 67944

Other (OTH) AF: 0.626 AC: 1323 AN: 2112

Alfa AF: 0.656 Hom.: 73264

Bravo AF: 0.622

Asia WGS AF: 0.390 AC: 1358 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.024
DANN	Benign	0.68
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs3758391; hg19: chr10-69643342;