3-107486895-C-T

Variant names:

• chr3-107486895-C-T
• rs1299704

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 0.624 in 151,982 control chromosomes in the GnomAD database, including 30,450 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 0.62 (30450 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

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 = 0.845 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: 0.623 AC: 94666 AN: 151864 Hom.: 30399 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.624 AC: 94773 AN: 151982 Hom.: 30450 Cov.: 32 AF XY: 0.624 AC XY: 46357 AN XY: 74262

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.589

Alfa AF: 0.571 Hom.: 12993

Bravo AF: 0.628

Asia WGS AF: 0.743 AC: 2585 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	2.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1299704; hg19: chr3-107205742;