rs10023987

Variant names:

• chr4-96969702-T-C
• rs10023987

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 0.216 in 151,558 control chromosomes in the GnomAD database, including 3,857 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 0.22 (3857 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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: 0.216 AC: 32706 AN: 151438 Hom.: 3851 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.216 AC: 32725 AN: 151558 Hom.: 3857 Cov.: 31 AF XY: 0.214 AC XY: 15830 AN XY: 74052

African (AFR) AF: 0.300 AC: 12390 AN: 41238

American (AMR) AF: 0.173 AC: 2626 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3468

East Asian (EAS) AF: 0.123 AC: 629 AN: 5124

South Asian (SAS) AF: 0.256 AC: 1227 AN: 4796

European-Finnish (FIN) AF: 0.115 AC: 1205 AN: 10484

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13006 AN: 67918

Other (OTH) AF: 0.237 AC: 499 AN: 2106

Alfa AF: 0.201 Hom.: 605

Bravo AF: 0.224

Asia WGS AF: 0.197 AC: 681 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs10023987; hg19: chr4-97890853;