rs10106243

Variant names:

• chr8-20486389-A-G
• rs10106243

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 0.231 in 152,158 control chromosomes in the GnomAD database, including 5,998 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 0.23 (5998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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: 0.231 AC: 35105 AN: 152038 Hom.: 5980 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0479

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.231 AC: 35186 AN: 152158 Hom.: 5998 Cov.: 32 AF XY: 0.228 AC XY: 16950 AN XY: 74414

African (AFR) AF: 0.473 AC: 19595 AN: 41460

American (AMR) AF: 0.258 AC: 3935 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3472

East Asian (EAS) AF: 0.198 AC: 1026 AN: 5170

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4826

European-Finnish (FIN) AF: 0.0479 AC: 509 AN: 10624

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7862 AN: 68006

Other (OTH) AF: 0.217 AC: 458 AN: 2114

Alfa AF: 0.148 Hom.: 1349

Bravo AF: 0.261

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.67
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10106243; hg19: chr8-20343900;