rs3098808

Variant names:

• chr4-99335667-G-A
• rs3098808

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 0.954 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.988 AC: 41067 AN: 41560

American (AMR) AF: 0.966 AC: 14759 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3147 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5172 AN: 5176

South Asian (SAS) AF: 0.943 AC: 4545 AN: 4820

European-Finnish (FIN) AF: 0.963 AC: 10224 AN: 10622

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63261 AN: 68034

Other (OTH) AF: 0.950 AC: 2010 AN: 2116

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
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs3098808; hg19: chr4-100256824;