rs1398240

chr8-23644093-C-Achr8-23644093-C-G

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 0.549 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.548

Alfa AF: 0.583 Hom.: 22029

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1398240; hg19: chr8-23501606;