rs2453998

Variant names:

• chr8-103077390-C-A
• rs2453998

Your query was ambiguous. Multiple possible variants found:

• chr8-103077390-C-A
• chr8-103077390-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;