5-119450451-A-T

Variant names:

• chr5-119450451-A-T
• rs28943585

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 0.105 in 152,160 control chromosomes in the GnomAD database, including 1,019 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 0.10 (1019 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 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: 0.105 AC: 15941 AN: 152042 Hom.: 1018 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0990

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.105 AC: 15946 AN: 152160 Hom.: 1019 Cov.: 32 AF XY: 0.103 AC XY: 7661 AN XY: 74386

African (AFR) AF: 0.0438 AC: 1819 AN: 41520

American (AMR) AF: 0.105 AC: 1606 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3468

East Asian (EAS) AF: 0.0987 AC: 511 AN: 5178

South Asian (SAS) AF: 0.146 AC: 702 AN: 4820

European-Finnish (FIN) AF: 0.100 AC: 1063 AN: 10592

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

European-Non Finnish (NFE) AF: 0.136 AC: 9260 AN: 67974

Other (OTH) AF: 0.116 AC: 244 AN: 2110

Alfa AF: 0.0735 Hom.: 107

Bravo AF: 0.103

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.85
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs28943585; hg19: chr5-118786146;