rs1869839

Variant names:

• chr7-114717488-A-G
• rs1869839

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.117 AC: 4860 AN: 41436

American (AMR) AF: 0.221 AC: 3370 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3470

East Asian (EAS) AF: 0.133 AC: 685 AN: 5154

South Asian (SAS) AF: 0.292 AC: 1401 AN: 4798

European-Finnish (FIN) AF: 0.386 AC: 4063 AN: 10518

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25672 AN: 67890

Other (OTH) AF: 0.259 AC: 546 AN: 2110

Alfa AF: 0.337 Hom.: 39432

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1869839; hg19: chr7-114357543;