rs1869839

chr7-114717488-A-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 0.275 in 151,828 control chromosomes in the GnomAD database, including 6,868 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 0.28 (6868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 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: 0.275 AC: 41774 AN: 151710 Hom.: 6867 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.275 AC: 41777 AN: 151828 Hom.: 6868 Cov.: 32 AF XY: 0.274 AC XY: 20310 AN XY: 74186

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.259

Alfa AF: 0.347 Hom.: 19142

Bravo AF: 0.253

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.13
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869839; hg19: chr7-114357543;