10-30500659-T-C

Variant names:

• chr10-30500659-T-C
• rs3124199

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 0.61 in 151,866 control chromosomes in the GnomAD database, including 28,967 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 0.61 (28967 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92460 AN: 151748 Hom.: 28914 Cov.: 30

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.610 AC: 92573 AN: 151866 Hom.: 28967 Cov.: 30 AF XY: 0.607 AC XY: 45063 AN XY: 74198

African (AFR) AF: 0.753 AC: 31170 AN: 41414

American (AMR) AF: 0.630 AC: 9617 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1823 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2674 AN: 5146

South Asian (SAS) AF: 0.512 AC: 2459 AN: 4800

European-Finnish (FIN) AF: 0.557 AC: 5868 AN: 10532

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37139 AN: 67926

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.568 Hom.: 41381

Bravo AF: 0.624

Asia WGS AF: 0.533 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.76
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs3124199; hg19: chr10-30789588;