10-101219798-C-T

Variant names:

• chr10-101219798-C-T
• rs35999315

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 0.193 in 152,058 control chromosomes in the GnomAD database, including 3,702 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 0.19 (3702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 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: 0.193 AC: 29270 AN: 151940 Hom.: 3700 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.193 AC: 29273 AN: 152058 Hom.: 3702 Cov.: 32 AF XY: 0.188 AC XY: 13935 AN XY: 74318

African (AFR) AF: 0.0556 AC: 2306 AN: 41502

American (AMR) AF: 0.176 AC: 2692 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3468

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5182

South Asian (SAS) AF: 0.0822 AC: 395 AN: 4808

European-Finnish (FIN) AF: 0.244 AC: 2575 AN: 10566

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

European-Non Finnish (NFE) AF: 0.291 AC: 19741 AN: 67938

Other (OTH) AF: 0.191 AC: 404 AN: 2112

Alfa AF: 0.233 Hom.: 640

Bravo AF: 0.184

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.88
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs35999315; hg19: chr10-102979555;