rs2447876

Positions:

• chr5-36028098-C-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 0.831 in 151,740 control chromosomes in the GnomAD database, including 52,602 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 0.83 (52602 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.902 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: 0.831 AC: 126021 AN: 151622 Hom.: 52565 Cov.: 28

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.831 AC: 126108 AN: 151740 Hom.: 52602 Cov.: 28 AF XY: 0.834 AC XY: 61875 AN XY: 74154

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.836

Alfa AF: 0.851 Hom.: 92346

Bravo AF: 0.823

Asia WGS AF: 0.867 AC: 3019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2447876; hg19: chr5-36028200;