rs2389886

Positions:

• chr4-119649267-G-A
• chr4-119649267-G-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 0.245 in 151,932 control chromosomes in the GnomAD database, including 5,000 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 0.24 (5000 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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: 0.245 AC: 37162 AN: 151814 Hom.: 4995 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.245 AC: 37175 AN: 151932 Hom.: 5000 Cov.: 32 AF XY: 0.243 AC XY: 18024 AN XY: 74224

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.264

Alfa AF: 0.260 Hom.: 965

Bravo AF: 0.252

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2389886; hg19: chr4-120570422;