8-23893638-C-T

Variant names:

• chr8-23893638-C-T
• rs10109414

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.366

Alfa AF: 0.400 Hom.: 15573

Bravo AF: 0.358

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.75
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10109414; hg19: chr8-23751151;