rs2851028

Positions:

• chr4-99435861-G-A

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 0.86 in 153,630 control chromosomes in the GnomAD database, including 57,646 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 0.86 (57165 hom., cov: 32)
  • Exomes 𝑓: 0.82 (481 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.99435861G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130918 AN: 152108 Hom.: 57110 Cov.: 32

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.861

GnomAD4 exome AF: 0.825 AC: 1158 AN: 1404 Hom.: 481 AF XY: 0.824 AC XY: 577 AN XY: 700

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.823

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.800

Gnomad4 NFE exome AF: 0.837

Gnomad4 OTH exome AF: 0.879

GnomAD4 genome AF: 0.861 AC: 131030 AN: 152226 Hom.: 57165 Cov.: 32 AF XY: 0.859 AC XY: 63959 AN XY: 74424

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.860

Alfa AF: 0.844 Hom.: 68398

Bravo AF: 0.857

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2851028; hg19: chr4-100357018;