3-98536548-T-G

Position:

• chr3-98536548-T-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 0.588 in 152,114 control chromosomes in the GnomAD database, including 27,550 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 0.59 (27550 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.861

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89420 AN: 151996 Hom.: 27551 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.588 AC: 89440 AN: 152114 Hom.: 27550 Cov.: 33 AF XY: 0.593 AC XY: 44085 AN XY: 74364

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.603

Alfa AF: 0.635 Hom.: 57185

Bravo AF: 0.585

Asia WGS AF: 0.648 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1350790; hg19: chr3-98255392;