rs2447876

Variant names:

• chr5-36028098-C-T
• rs2447876

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 0.831 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
• Publications: 4 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.756 AC: 31280 AN: 41360

American (AMR) AF: 0.853 AC: 13026 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3086 AN: 3464

East Asian (EAS) AF: 0.816 AC: 4156 AN: 5096

South Asian (SAS) AF: 0.925 AC: 4439 AN: 4800

European-Finnish (FIN) AF: 0.886 AC: 9350 AN: 10550

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58073 AN: 67890

Other (OTH) AF: 0.836 AC: 1755 AN: 2100

Alfa AF: 0.847 Hom.: 217476

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2447876; hg19: chr5-36028200;