rs1870007

Positions:

• chr3-108256485-A-G
• chr3-108256485-A-T

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 0.696 in 152,078 control chromosomes in the GnomAD database, including 37,087 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 0.70 (37087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.696 AC: 105718 AN: 151960 Hom.: 37047 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.696 AC: 105810 AN: 152078 Hom.: 37087 Cov.: 32 AF XY: 0.697 AC XY: 51837 AN XY: 74354

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.724

Alfa AF: 0.689 Hom.: 33677

Bravo AF: 0.707

Asia WGS AF: 0.803 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870007; hg19: chr3-107975332;