5-119451974-C-A

Variant names:

• chr5-119451974-C-A
• rs28943586

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 0.0992 in 152,264 control chromosomes in the GnomAD database, including 983 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 0.099 (983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 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: 0.0992 AC: 15099 AN: 152146 Hom.: 982 Cov.: 32

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.0992 AC: 15100 AN: 152264 Hom.: 983 Cov.: 32 AF XY: 0.0977 AC XY: 7277 AN XY: 74446

African (AFR) AF: 0.0252 AC: 1046 AN: 41572

American (AMR) AF: 0.103 AC: 1575 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3470

East Asian (EAS) AF: 0.0966 AC: 501 AN: 5186

South Asian (SAS) AF: 0.145 AC: 698 AN: 4826

European-Finnish (FIN) AF: 0.100 AC: 1061 AN: 10604

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9241 AN: 67990

Other (OTH) AF: 0.112 AC: 237 AN: 2110

Alfa AF: 0.125 Hom.: 183

Bravo AF: 0.0967

Asia WGS AF: 0.114 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.71
DANN	Benign	0.81
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs28943586; hg19: chr5-118787669;