3-99345087-G-C

Variant names:

• chr3-99345087-G-C
• rs900060

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 0.157 in 151,934 control chromosomes in the GnomAD database, including 2,398 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 0.16 (2398 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 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: 0.157 AC: 23824 AN: 151816 Hom.: 2394 Cov.: 32

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.0178

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.157 AC: 23836 AN: 151934 Hom.: 2398 Cov.: 32 AF XY: 0.154 AC XY: 11424 AN XY: 74244

Gnomad4 AFR AF: 0.0574

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.162

Alfa AF: 0.0914 Hom.: 147

Bravo AF: 0.153

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs900060; hg19: chr3-99063931;