8-23644093-C-A

Variant names:

• chr8-23644093-C-A
• rs1398240

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 0.549 in 151,876 control chromosomes in the GnomAD database, including 23,278 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 0.55 (23278 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.549 AC: 83283 AN: 151758 Hom.: 23277 Cov.: 30

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.549 AC: 83306 AN: 151876 Hom.: 23278 Cov.: 30 AF XY: 0.546 AC XY: 40499 AN XY: 74216

African (AFR) AF: 0.457 AC: 18950 AN: 41422

American (AMR) AF: 0.557 AC: 8502 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2083 AN: 3464

East Asian (EAS) AF: 0.695 AC: 3578 AN: 5146

South Asian (SAS) AF: 0.570 AC: 2736 AN: 4800

European-Finnish (FIN) AF: 0.508 AC: 5347 AN: 10526

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40278 AN: 67942

Other (OTH) AF: 0.548 AC: 1153 AN: 2104

Alfa AF: 0.583 Hom.: 30590

Bravo AF: 0.550

Asia WGS AF: 0.571 AC: 1989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.6
DANN	Benign	0.81
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1398240; hg19: chr8-23501606;