rs2453998

chr8-103077390-C-Achr8-103077390-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 0.958 in 152,272 control chromosomes in the GnomAD database, including 69,921 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 0.96 (69921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.958 AC: 145764 AN: 152154 Hom.: 69866 Cov.: 32

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.956

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

GnomAD4 genome AF: 0.958 AC: 145878 AN: 152272 Hom.: 69921 Cov.: 32 AF XY: 0.959 AC XY: 71417 AN XY: 74456

Gnomad4 AFR AF: 0.979

Gnomad4 AMR AF: 0.968

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.956

Alfa AF: 0.943 Hom.: 31524

Bravo AF: 0.962

Asia WGS AF: 0.949 AC: 3300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.51
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2453998; hg19: chr8-104089618;