8-23893638-C-T

Variant names:

• chr8-23893638-C-T
• rs10109414

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 0.367 in 151,698 control chromosomes in the GnomAD database, including 10,569 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 0.37 (10569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692
• Publications: 33 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 = 0.414 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: 0.367 AC: 55640 AN: 151580 Hom.: 10571 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.367 AC: 55657 AN: 151698 Hom.: 10569 Cov.: 32 AF XY: 0.363 AC XY: 26907 AN XY: 74122

African (AFR) AF: 0.325 AC: 13423 AN: 41308

American (AMR) AF: 0.309 AC: 4714 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1398 AN: 5152

South Asian (SAS) AF: 0.138 AC: 665 AN: 4818

European-Finnish (FIN) AF: 0.457 AC: 4794 AN: 10488

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28406 AN: 67908

Other (OTH) AF: 0.366 AC: 773 AN: 2112

Alfa AF: 0.397 Hom.: 37983

Bravo AF: 0.358

Asia WGS AF: 0.225 AC: 783 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	0.75
DANN	Benign	0.33
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs10109414; hg19: chr8-23751151;