rs1994882

Variant names:

• chr5-39806062-C-A
• rs1994882

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 0.627 in 151,898 control chromosomes in the GnomAD database, including 31,260 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 0.63 (31260 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.820
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 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: 0.627 AC: 95218 AN: 151778 Hom.: 31252 Cov.: 31

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.627 AC: 95264 AN: 151898 Hom.: 31260 Cov.: 31 AF XY: 0.620 AC XY: 46051 AN XY: 74220

African (AFR) AF: 0.476 AC: 19682 AN: 41380

American (AMR) AF: 0.584 AC: 8912 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1175 AN: 5140

South Asian (SAS) AF: 0.657 AC: 3160 AN: 4808

European-Finnish (FIN) AF: 0.680 AC: 7170 AN: 10548

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50383 AN: 67970

Other (OTH) AF: 0.653 AC: 1380 AN: 2112

Alfa AF: 0.695 Hom.: 120765

Bravo AF: 0.609

Asia WGS AF: 0.452 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.47
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs1994882; hg19: chr5-39806164;