rs3098808

chr4-99335667-G-A

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 0.954 in 152,292 control chromosomes in the GnomAD database, including 69,398 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 0.95 (69398 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.98 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: 0.954 AC: 145201 AN: 152174 Hom.: 69344 Cov.: 32

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.954 AC: 145315 AN: 152292 Hom.: 69398 Cov.: 32 AF XY: 0.956 AC XY: 71156 AN XY: 74456

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.966

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.943

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.950

Alfa AF: 0.947 Hom.: 8473

Bravo AF: 0.957

Asia WGS AF: 0.981 AC: 3413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.1
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3098808; hg19: chr4-100256824;