5-4199820-C-G

Variant names:

• chr5-4199820-C-G
• rs10036225

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 0.941 in 152,286 control chromosomes in the GnomAD database, including 67,529 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 0.94 (67529 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.941 AC: 143204 AN: 152168 Hom.: 67489 Cov.: 33

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.941 AC: 143297 AN: 152286 Hom.: 67529 Cov.: 33 AF XY: 0.942 AC XY: 70113 AN XY: 74446

African (AFR) AF: 0.896 AC: 37226 AN: 41550

American (AMR) AF: 0.961 AC: 14703 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3361 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5122 AN: 5152

South Asian (SAS) AF: 0.892 AC: 4305 AN: 4828

European-Finnish (FIN) AF: 0.983 AC: 10442 AN: 10620

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 65010 AN: 68040

Other (OTH) AF: 0.933 AC: 1972 AN: 2114

Alfa AF: 0.954 Hom.: 3254

Bravo AF: 0.940

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.29
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10036225; hg19: chr5-4199933;